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"write.project","write.project","write.table","writing a pdb file","x ray","xi","xi", "xstick","xstick","xstick","xyz","zoom","zoom","zoom","zoom","zoom","zoom","zoom", "zoom"); var titles=new Array("Customized Label 2D or 3D","Display and Convert Molecule","Chemical View Options", "Pharmacophore","Convert Structure to Smiles","2D Depiction","Align/Color by 2D Scaffold", "2D and 3D Labels","Convert Smiles to 2D","2D and 3D Labels","2D Depiction","Customized Label 2D or 3D", "Display and Convert Molecule","Chemical View Options","Set Chemical Table 3D Browse Mode", "Pharmacophore","2D Depiction","2D and 3D Labels","How to add and sample new substiutents to your ligand in the ICM 3D Ligand Editor.", "How to display energy atomic circles in the ICM 3D Ligand Editor.","How to begin editing your ligand in the ICM 3D Ligand Editor.", "How to center on a ligand in the ICM 3D Ligand Editor.","How to configure the default display in the ICM 3D Ligand Editor.", "How to re-dock a ligand in the ICM 3D Ligand Editor.","How to restrain (tether) atoms during docking.", "How to edit the ligand in 2D in the ICM 3D Ligand Editor.","How to sample linkers between two chemical fragments.", "How to display and undisplay hydrogen atoms in the ICM 3D Ligand Editor.","How to display hydrogen bonds in the ICM 3D ligand editor.", "How to setup the ligand in the ICM 3D Ligand Editor.","How to perform ligand minimization in the ICM 3D Ligand Editor.", "How to sample more than one substituent at a time in the ICM 3D Ligand Editor.", "How to change the 3D Ligand Editor preferences.","How to change the size of the ligand binding pocket - change purple box size.", "How to setup the receptor in the ICM 3D Ligand Editor.","How to add an edited ligand to a chemical spreadsheet (table).", "How to screen databases of chemical substituents.","How to display and undisplay the ligand surface representation in the ICM 3D Ligand Editor.", "How to undo and redo changes in the ICM 3D Ligand Editor.","How to display unsatisfied hydrogen bonds in the ICM 3D Ligand Editor.", "Mesh Options.","Multiple Receptor Conformation Ensemble Docking Example","MolCart installation error on 64Bit machines", "Multiple APF Alignment of Compounds in a Table","Flexible APF Superposition to Template from Table", "Export as ActiceICM Html","How do I color ribbon models according to Optimal Docking Area (ODA)", "Graphics Preferences","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "System Preferences","I would like to have a local copy of the NCBI Blast database- any advice?", "Directories Preferences","Labeling Residues","Load","Display Tab","Structure Representation", "Shell Preferences","Constructing New Protein and Nucleic Acid Sequences","Six Frame Translation", "Working with Sequences","How do I color ribbon models according to Optimal Docking Area (ODA)", "Directories Preferences","How do I color ribbon models according to Optimal Docking Area (ODA)", "Directories Preferences","Directories Preferences","Directories Preferences","Directories Preferences", "System Preferences","System Preferences","System Preferences","Directories Preferences", "System Preferences","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Frequently Asked Questions","Write Image","Movie Making","Movie Making Options", "Graphics Preferences","GUI Preferences","GUI Preferences","Font Preferences","Bonds Preferences", "Graphics Preferences","Graphics Preferences","Graphics Preferences","Graphics Preferences", "Graphics Preferences","Graphics Preferences","GUI Preferences","Font Preferences", "Graphics Preferences","Bonds Preferences","Ribbon Preferences","Ribbon Preferences", "Ribbon Preferences","Ribbon Preferences","Ribbon Preferences","Ribbon Preferences", "Font Preferences","Font Preferences","Font Preferences","Graphics Preferences","Bonds Preferences", "Bonds Preferences","Bonds Preferences","Bonds Preferences","Bonds Preferences","Bonds Preferences", "Bonds Preferences","Bonds Preferences","Graphics Preferences","Graphics Preferences", "Graphics Preferences","Graphics Preferences","Graphics Preferences","Graphics Preferences", "GUI Preferences","Font Preferences","Graphics Preferences","Ribbon Preferences", "Ribbon Preferences","Ribbon Preferences","GUI Preferences","GUI Preferences","GUI Preferences", "Graphics Preferences","Font Preferences","Font Preferences","Font Preferences","Graphics Preferences", "Bonds Preferences","Graphics Preferences","Graphics Preferences","Graphics Preferences", "Graphics Preferences","Bonds Preferences","Ribbon Preferences","Bonds Preferences", "Bonds Preferences","Bonds Preferences","Bonds Preferences","Graphics Preferences", "Graphics Preferences","Graphics Preferences","Graphics Preferences","Graphics Preferences", "Introduction","How To?","GUI Preferences","GUI Preferences","ICM and AutoSave","ICM and AutoSave", "System Preferences","System Preferences","GUI Preferences","System Preferences", "System Preferences","GUI Preferences","GUI Preferences","GUI Preferences","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "System Preferences","System Preferences","System Preferences","Display PDB Header", "System Preferences","General Preferences","Introduction","ICM graphics crashes.", "Image Preferences","Image Preferences","Image Preferences","Image Preferences","Image Preferences", "Image Preferences","Image Preferences","Image Preferences","Image Preferences","Image Preferences", "Image Preferences","Image Preferences","Image Preferences","Image Preferences","Image Preferences", "Image Preferences","Image Preferences","How do I read in a small molecule from ISIS draw and convert it to 3D?", "IUPAC Chemical Nomenclature","Shell Preferences","Directories Preferences","Write Image", "Load","Directories Preferences","Learn and Predict","Learn and Predict","Molecular Tables", "Working with Chemistry Tools","Loading Chemical Structures","Molecular Table Display", "Display and Convert Molecule","Copy Molecule","Edit Molecule","Color Table Column", "Database File Format","Loading Chemical Structures","Database File Format","How to make a local database.", "GUI Preferences","Shell Preferences","Shell Preferences","How to decompose a library based on a Markush structure.", "How to create a Markush structure.","System Preferences","Calculate Properties", "Shell Preferences","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Calculate Properties","Calculate Properties","Query Processing","Calculate Properties", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "How to Build Fully-Interactive 3D Molecular Documents (iSee File)","GUI Preferences", "GUI Preferences","GUI Preferences","I would like to have a local copy of the NCBI Blast database- any advice?", "Searching the PDB","Calculate Properties","Calculate Properties","Calculate Properties", "Calculate Properties","Calculate Properties","Calculate Properties","ICM graphics crashes.", "How do I color ribbon models according to Optimal Docking Area (ODA)","How do I color ribbon models according to Optimal Docking Area (ODA)", "Directories Preferences","Running VLS Jobs in PBS UNIX Cluster Environment","Learn", "A little theory on learning","How to extract a 2D sketch of a ligand in complex with a PDB strcture.", "Biomolecule Generator","Loading Your PDB File","Display PDB Header","Converting PDB Files Into ICM Objects", "Load Sequence","Directories Preferences","Directories Preferences","PDB Search", "PDB Search by Field","PDB Search by Identity","PDB Search by Homology","PDB Search with External Seqeuence", "PDB Search by Field","PDB Search by Homology","PDB Search by Identity","PDB Search with External Seqeuence", "Converting PDB Files Into ICM Objects","Converting a PDB File into an ICM Object", "Querying PDB by Sequence Pattern","Querying PDB by Keyword or PDB Code","Querying PDB by Sequence Pattern", "Searching the PDB","Querying PDB by Keyword or PDB Code","Querying PDB by Sequence Pattern", "Sensitive PDB Similarity Searches","Working with PDB Search Results","PDB Searching", "Sensitive PDB Similarity Searches","Querying PDB by Sequence Pattern","Sensitive PDB Similarity Searches", "Load","Plot Preferences","Plot Preferences","Plot Preferences","Plot Preferences", "Plot Preferences","Plot Preferences","Plot Preferences","Plot Preferences","Plot Preferences", "Plot Preferences","Plot Preferences","Plot Preferences","Plot Preferences","Plot Preferences", "Plot Preferences","Learn","How to Make a Picture","Write Image","Movie Making","Movie Making Options", "Directories Preferences","Directories Preferences","How do I color ribbon models according to Optimal Docking Area (ODA)", "Directories Preferences","Learn and Predict","Learn","How to build a QSAR prediction model.", "How to apply a QSAR prediction model.","Generating Chemical Fragments","R-Group Decomposition", "I am docking a racemic compound how can I sample both R andS states during docking?", "Find and Replace","Superimpose","Ramachandran Plot Interactive","Shell Preferences", "Setup Receptor","Font Preferences","Font Preferences","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Learn and Predict","How to decompose a library based on a Markush structure.","Which score value should I use for analysis.", "I have a complex I wish to generate an ICM VLS Score for, however I did not dock it using VLS. How can I do this?", "Molecular Tables","Working with Chemistry Tools","Loading Chemical Structures","Display and Convert Molecule", "Copy Molecule","Edit Molecule","Color Table Column","Database File Format","GUI Preferences", "Font Preferences","Font Preferences","Font Preferences","GUI Preferences","GUI Preferences", "How to Import, Sketch, and Edit Chemicals","How to use SMILES strings to sketch a chemical.", "Saving in the Molecular Editor","Shell Preferences","Font Preferences","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "How to convert SMILES strings to 2D","Load","Directories Preferences","Directories Preferences", "Running VLS Jobs in PBS UNIX Cluster Environment","System Preferences","System Preferences", "System Preferences","System Preferences","System Preferences","Virtual Ligand Screening", "Virtual Ligand Screening","VLS Getting Started","Running VLS Jobs in PBS UNIX Cluster Environment", "How to Plot Histograms and Scatterplots of VLS Data","VLS Preferences","Font Preferences", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Shell Preferences","Bonds Preferences","Searching the PDB","Receptor Considerations", "Directories Preferences","Display Tab","Structure Representation","Light Tab","Property Monitor", "Constructing New Protein and Nucleic Acid Sequences","ActiveICM","When using ActiveICM is there a way to set a RELATIVE path to an icb file rath than ABSOLUTE?", "How to Embed in Microsoft PowerPoint 2003","ActiveICM","Using activeICM during a presentation", "Advanced use of activeICM: Macros to direct visualisation changes","PowerPoint Cache Errors", "Advanced use of activeICM: Macros to direct visualisation changes","How to Change ActiveICM Component Properties", "Learn and Predict","Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "Molcart Administration","Select by Consensus","A dictionary of chemical groups.", "How to Drag and Drop","How to Make a Sequence Alignment","Alignment Introduction", "Align/Color by 2D Scaffold","Pairwise Alignments","Align/Color by 2D Scaffold","Align DNA to Protein", "Align Multiple Sequences","Align Two Sequences","Align DNA vs Protein","Align DNA to Protein", "Boxing Shading and Annotating an Alignment","Boxing Shading and Annotating an Alignment", "Align Multiple Sequences","Multiple Sequence Alignments","Sequence Alignments","Drag and Drop", "Boxing Shading and Annotating an Alignment","Align Two Sequences","Align Two Sequences", "How to Make an Alignment using Drag and Drop","How do I show the sequence conservation around the ligand binding site?", "Ligand Binding Pocket Analysis Examples","Displaying the sequence conservation around the ligand binding site.", "Add a Comment","Edit an Alignment","Alignment Editor","Load Example Alignment","How to change font size in html-documents, alignments, terminal, table, graphics?", "Alignment Gaps","Alignment Gaps","Alignment Introduction","Reorder Sequences","Searching an Alignment", "Making Alignment Selections","Alignment View Options","Shading and Boxing an Alignment", "Coloring an Alignment.","Shading and Boxing an Alignment","Add a Comment","Coloring an Alignment.", "Select by Consensus","Cut Vertical Alignment Block","Save, Print and Delete","Alignment View Options", "Alignment Editor","Sequence Drag and Drop and the Alignment Editor","Extract Sub-Alignment As Is", "Alignment Gaps","Alignment View Options","Linked Alignments and Structures","Multiple Sequence Alignment", "Alignment View Options","Save, Print and Delete","Alignment View Options","Reorder Sequences", "Alignment View Options","Save, Print and Delete","Searching an Alignment","Making Alignment Selections", "Basic Alignment Selections","Select by Consensus","Alignment View Options","Shading and Boxing an Alignment", "Alignment View Options","Alignment View Options","How to Work With Sequences and Alignments", "Sequence Alignments","Working with Sequences and Alignments","Light Tab","Image Preferences", "Light Tab","Constructing New Protein and Nucleic Acid Sequences","Bioinfo Menu", "Planar Angle","Dihedral Angle","Torsion Angles","Label Variables","How can I display the dihedral angle?", "How can I change the torsion angle?","How to Measure the Distance Between Two Atoms.", "How can I calculate the RMSD between two protein structures?","Animate View","Animate View", "Molecular Animations and Transitions","Make Animation","Change Speed, Range and Cycle Length of Animation", "Interrupt Animation","Saving an Animation","Saving an Animation","Making Molecular Animations, Slides, and Documents", "Annotate By Substructure","Annotation","Annotate By Substructure","Labeling and Annotation", "Annotation","Write Image","Full Scene Antialias","Antialias Lines","Antialias Lines", "Is there a way to build a classification model using the APF output?","Flexible APF Superposition to Template from Table", "Multiple APF Alignment of Compounds in a Table","Is there a way to build a classification model using the APF output?", "Append Rows","Predict","Protein Interface by ODA","Contact Areas","Protein-Protein Docking", "Optimal Docking Area","Protein-Protein Docking Procedure","Chemical View Options", "How to Arrange Windows","How to Arrange Windows","Annotation","What does as_graph mean?", "What does as_graph mean?","Optimize H, His, Asn, Gln and Pro","Optimize H,His,Asn,Gln,Pro", "Ribbon Representation","2D Depiction","Assign Helices and Strands","Assign Helices and Strands", "General Preferences","Chemical View Options","Chemical View Options","How do I specify a particular color for only the carbon atoms of a molecules?", "I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "What does as_graph mean?","How can I change the color of a grob atom based surface according to the underlying atom coloring scheme?", "How can I display more information regarding an atom such as mmff type and charge?", "How do I display the distance between two atoms?","Making Basic Selections","Making Sequence Selections in the ICM Workspace", "Labeling and Annotation","Label Atoms","Label Atoms","How do I set a formal charge?", "Font Preferences","Right Click Options","Query Setup","Enumerate by Scaffold","How to Change ActiveICM Component Properties", "ICM X-Ray AutoFit - Automated Model Building into Density","ICM and AutoSave","Cluster", "Movie Making","Movie Making Options","Screen-grabbing Movie","Grid and Axis Display", "Change Axis Data","Axis Options","Axis Options","Axis Options","Axis Options","Local Flexibility", "Receptor Considerations","PDB Preparation - Occupancy and B-Factors","How can I select only the backbone atoms?", "Coloring Background","Background Image","Molecule and Background Coloring","How to change the background color with one click?", "Background Image","Restore Recent Backup","Calculate Properties","Property Monitor", "General Preferences","Display Tab","Structure Representation","Searching the PDB", "Basic Alignment Selections","Basic Selections","Batch Docking","Running VLS Jobs in PBS UNIX Cluster Environment", "Protein-Protein Docking Batch","How do I turn off the annoying beep?","Begin the Docking Simulation", "Rotate Chemical for Best-Fit","How to Display Electrostatic Surfaces Around a Ligand.", "How can I find out which residues are surrounding a ligand binding pocket?","I do not have ICM-VLS but I would like to calculate the binding energy of my docked complex - how can I do this?", "How do I identify the binding pockets in my receptor?","Ligand Binding Pocket Analysis Examples", "Align DNA vs Protein","Multiple Sequence Alignment","Align Two Sequences","Link to Structure", "Predict Secondary Structure","Six Frame Translation","Biomolecule Generator","Tools Menu - Xray", "Biomolecule Generator","Biomolecule Generator","Crystallographic Analysis Tools", "Biomolecule Generator","MolCart installation error on 64Bit machines","Search and Align", "How do I sample flexible ring conformations (boat, chair etc..) during docking?", "How to Convert a Chemical from the PDB","How to Display Hydrogen Bonds Between a Ligand and Receptor.", "Making a disulfide bond.","Editing structure using keyboard","How do I change the bond types and add formal charges to a ligand from the PDB?", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Displaying hydrogen bonds between a ligand and receptor.","How do I make a covalent bond between a ligand and a receptor?", "Converting a Chemical from the PDB using the ICM Workspace","How to Convert a Chemical from the PDB using the Graphical Display", "Converting a Chemical from the PDB","Converting a Chemical from the PDB using the ICM Workspace", "Converting a Chemical from the PDB using the Graphical Display","Hydrogen Bonding", "Bonds Preferences","Box","Box","Font Preferences","Display Rainbow, Box, Ruler", "When I view my docking run my ligand never jumps into the box - what did I do wrong?", "Making an amino acid mutation","How to remove chain breaks (dotted lines)","Set Chemical Table 3D Browse Mode", "Results - Scan Hits","Set Chemical Table 3D Browse Mode","Browse Database","Stack", "Troubleshooting","How to Access the ICM Molecular Editor","Make Animation","Build Model", "Edit Structure","Advanced use of activeICM: Macros to direct visualisation changes", "Quit","PowerPoint Cache Errors","How to Measure the Distance Between Two Atoms.", "I do not have ICM-VLS but I would like to calculate the binding energy of my docked complex - how can I do this?", "Calculate Properties","I am having problems with my ICM script when running from the unix command line.", "How do I specify a particular color for only the carbon atoms of a molecules?","I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "Generate 3D Conformers","Closed Cavities","How do I load an electron density map into ICM?", "How can I contour an electron density map and adjust contour levels and color?", "Crystallographic Cell","How to Move a Structure in the Graphical Display","Center", "Move Buttons","Center","Center","Change Column Format","How can I select the closest residue from the center of mass of a selected residue?", "Tree Selection","How to remove the dotted lines in chain breaks.","Find Related Chains", "How do I sample flexible ring conformations (boat, chair etc..) during docking?", "How do I sample conformations of flexible rings in docked ligands, for example, a \"chair-boat\" transition?", "Altering a Selection","Change Speed, Range and Cycle Length of Animation","Alignment Editor", "How to Convert a Chemical from the PDB","Converting a Chemical from the PDB using the ICM Workspace", "How to Convert a Chemical from the PDB using the Graphical Display","Electrostatic potential", "Labeling Atoms","Right Click Options","Query Setup","Converting a Chemical from the PDB", "Converting a Chemical from the PDB using the ICM Workspace","Converting a Chemical from the PDB using the Graphical Display", "How do I change the bond types and add formal charges to a ligand from the PDB?", "How can I convert a chemical in a chemical table into 3D?","Saving Chemical Structures and Images", "Saving in the Molecular Editor","Saving Chemical Images","Saving from a chemical table.", "Saving in the ICM Workspace","Superposition","Chemical View Options","How to Access the ICM Molecular Editor", "Cluster","Working with Chemistry Tools","Chemical Display","Chemical View Options", "Zoom, Translate and Z-rotate a Chemical in a table.","Set Chemical Table 3D Browse Mode", "Rotate Chemical for Best-Fit","Color Chemical Structure","Editing structure using keyboard", "Generating Chemical Fragments","Molcart Search","2D Depiction","Generate Tautomers", "Enumerate by Scaffold","Enumerate by Reaction","Superposition","How can I change the layout of a chemical table?", "How can I convert a chemical in a chemical table into 3D?","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I have a small molecule displayed in 3D in a loaded PDB file. How can I extract this molecule into an ICM Chemical Table?", "What is considered a good druglikeness value?","I do not see the chemical property monitor in the molecular editor. Where is it?", "Cluster Set","A dictionary of chemical groups.","Reading Chemical Structures","Molecular Editor", "Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "ICM crashes, or hangs if you are trying to start the Chemical Editor, or a Query window", "Find and Replace","Split Chemical(s) into Fragments","A dictionary of chemical groups.", "A dictionary of chemical groups.","Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "Right Click Options","Chemical Search","Filter Search","Search a Database by Text", "Chemical Smiles","How to Import, Sketch, and Edit Chemicals","How to rotate a 2D chemical sketch so it fits nicely in its cell in a chemical table?", "How to compare two chemical spreadsheets.","Working with Chemical Spreadsheets.", "Working with Chemistry Tools","How to use Atomic Property Fields for Chemical Superposition", "How to Perform Rigid and Flexible Chemical Substructure Superposition.","How to convert SMILES strings to 2D", "Molecular Table Display","Molecular Tables","How to save a 2D sketch into a chemical spreadsheet.", "Convert to 3D","Convert to 3D","Save and Append Chemical Structures","How to perform chemical clustering.", "Cluster Set","How to Convert a Chemical from the PDB","Converting a Chemical from the PDB using the ICM Workspace", "How to Convert a Chemical from the PDB using the Graphical Display","ICM Convert", "Convert to 3D","Converting a Chemical from the PDB","Converting a Chemical from the PDB using the ICM Workspace", "Converting a Chemical from the PDB using the Graphical Display","How do I change the bond types and add formal charges to a ligand from the PDB?", "How to rotate a 2D chemical sketch so it fits nicely in its cell in a chemical table?", "Drawing a New Chemical Structure","Draw Chemical","How to identify duplicate chemicals in a chemical spreadsheet.", "How to Import, Sketch, and Edit Chemicals","Editing a Chemical Structure","Edit Chemical", "Saving Chemical Structures and Images","Saving from a chemical table.","Saving in the Molecular Editor", "Saving in the ICM Workspace","Saving Chemical Images","Reading Chemical Structures", "Loading Chemical Structures","Merge Two Sets","IUPAC Chemical Nomenclature","Drawing a New Chemical Structure", "How to calculate chemical properties in a chemical spreadsheet.","Right Click Options", "Query Setup","Query Processing","Reading Chemical Structures","Loading Chemical Structures", "Undo and Redo","Save and Append Chemical Structures","Saving Chemical Structures and Images", "Saving from a chemical table.","Saving in the Molecular Editor","Saving in the ICM Workspace", "Saving Chemical Images","How to setup a chemical search.","How to search chemical spreadsheets, local databases and MolCart.", "How to send a chemical search query.","Right Click Options","Chemical Search","Query Setup", "Query Processing","Chemical Similarity Searching","Advanced Chemical Similarity Searching", "How to add conditions to your chemical search.","How to draw a chemical search query.", "Right Click Options","Chemical Search","Query Setup","Query Processing","Chemical Similarity Searching", "Advanced Chemical Similarity Searching","How to Import, Sketch, and Edit Chemicals", "How to sketch chemicals in the ICM Molecular Editor.","Chemical Smiles","Working with Chemical Spreadsheets.", "Saving Chemical Structures and Images","Saving from a chemical table.","Saving in the Molecular Editor", "Saving in the ICM Workspace","Saving Chemical Images","Loading Chemical Structures", "Save and Append Chemical Structures","Editing a Chemical Structure","Advanced Chemical Similarity Searching", "Rigid Superposition of Compounds in a Table onto a Template in The Graphical Display", "Rigid Substructure Superposition","Flexible Substructure Superposition","Flexible APF Superposition to Template from Table", "Multiple APF Alignment of Compounds in a Table","Molecular Tables","Working with Chemical Spreadsheets.", "Draw Chemical","Edit Chemical","Undo and Redo","Working with Chemical Spreadsheets.", "FAQ-Cheminformatics","Generate Tautomers","FAQ-Cheminformatics","Chemistry Menu", "Convert Smiles to 2D","Select Duplicates","Select Duplicates","MolCart installation error on 64Bit machines", "Label Variables","How can I display the dihedral angle?","Generate Stereoismers", "Generate Stereoismers","Generate Stereoismers","General Preferences","Display Clash", "Display Clash","Chemical View Options","Clear-Display-and-Planes","Clear-Display-and-Planes", "How to: Right Click Options","Keyboard and Mouse Shortcuts","Move Buttons","Mesh Clipping", "Mesh Clipping","The front and back part of my structure have been clipped away how do I restore these regions in my display.", "Save and Print Tree","I would like to create a movie wherein I \"walk\" through the molecule by moving the front clipping plane to the end. Can I write a loop that moves the clipping and generates an image after every step to generate my movie afterwards?", "How to use the Graphics window controls","Graphics and View Tools","Clipping Tools", "Clipping Tools","icmPocketFinder","Closed Cavities","Cluster","Cluster","Running VLS Jobs in PBS UNIX Cluster Environment", "How to select representative centers from a tree.","Data Clustering","Meshes Tab", "Google 3D Objects (Sketchup)","Protein Health","Coloring","Labeling Atoms","Labeling Residues", "Mark and Select Rows","Tree View","Color Chemical Structure","Align/Color by 2D Scaffold", "How do I specify a particular color for only the carbon atoms of a molecules?","I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "How can I change the color of a grob atom based surface according to the underlying atom coloring scheme?", "How do I color a structure by secondary structure?","Coloring and Changing Molecule Representations", "Molecule and Background Coloring","Ligand Binding Pocket Analysis Examples","Coloring an Alignment.", "Coloring Background","Color Chemical Structure","Color and Mesh Display","How do I color a structure by secondary structure?", "Color Table Column","How to color a 2D chemical sketch by pharmacophore feature.", "Color Background","Coloring Background","Displaying Distances","Color and Mesh Display", "Color Table Column","Coloring","Working with Tables","Change Column and Row Width", "Hide and Show Columns","Change Column Format","Plotting Table Data","Column Histogram", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "Change Column and Row Width","Column Statistics","Table Color","How to show and hide columns and rows in a chemical spreadsheet.", "How to show and hide columns and rows in a chemical spreadsheet.","How to enumerate a Markush library.", "Merge Two Sets","Ribbon Preferences","How can I run the docking simulation from the UNIX command line?", "How to check on the display status of an object in the command line.","Writing a Script in GUI.", "How can I write a script in the Graphical User Interface?","Chemical Table Side-by-Side View", "Compare Two Sets","Merge Two Sets","How to compare two chemical spreadsheets.","Compare Two Sets", "Save Project Compatible with ICM 3_5","Molecular Tables","Generate Tautomers","How can I download the MolCart vendor compounds provided by MolSoft?", "Image Preferences","Filter Search","Generate 3D Conformers","Generate 3D Conformers", "Multiple Receptor Conformation Docking","How do I view a stack of solutions after a simulations?", "Generate 3D Conformers","Move Buttons","Connect (Move)","Move and Resize Mesh","Connect (Move)", "Right Click Options","Query Setup","Find Related Chains","Ligand Binding Pocket Analysis Examples", "New","Constructing a New Peptide","Make Animation","Constructing New DNA or RNA", "Constructing New DNA or RNA","Constructing a New Compound","Constructing a New Compound", "New","Constructing New Protein and Nucleic Acid Sequences","New","Constructing New Protein and Nucleic Acid Sequences", "Constructing New Protein and Nucleic Acid Sequences","Contact Areas","Contact Areas", "Contour Electron Density Map","Convert Xray Density to Grid","Contour Electron Density Map", "How to Convert a Protein into an ICM Object","Converting PDB Files Into ICM Objects", "Convert to Racemic","How can I convert a chemical in a chemical table into 3D?", "How to generate 3D ligand conformers.","How to convert 2D chemical sketches to 3D.", "How to convert 2D sketches in the molecule editor into 3D.","Display and Convert Molecule", "Convert to 3D","Convert to Local Database","Converting a Chemical from the PDB", "How to convert SMILES strings to 2D","Convert to Local Database","Convert Smiles to 2D", "Convert Structure to Smiles","Convert Xray Density to Grid","Converting PDB Files Into ICM Objects", "Copy Cut and Paste Row","Copy Molecule","Isis Draw Copy and Paste","Pharmacophore Draw 3D", "Copy Cell","Copy Cell","Copy Molecule","Copy Cut and Paste Row","Copy, Cut and Paste", "Copy Cell","Copy Selection to an ICM Table","How to copy and paste 2D chemicals.", "CPK Representation","How can I display a structure in many different representations simultaneously?", "Molecule Representations","Restore Recent Backup","Creating a Molecular Document", "Editing a Molecular Document","Generate New Table","Create/Modify Markush","Creating a Molecular Document", "I have the XYZ origin cross displayed - How can I undisplay this?","Clipping Tools", "Crystallographic Cell","Crystallographic Analysis Tools","Crystallographic Cell", "Tools Menu - Xray","Crystallographic Neighbor","Tools Menu - Xray","Get Electron Density Map", "Contour Electron Density Map","Convert Xray Density to Grid","How do I load an electron density map into ICM?", "How can I contour an electron density map and adjust contour levels and color?", "Reading a Table","Saving a table","Save a Table","How can I store a view and return to it later?", "How to Change ActiveICM Component Properties","Move Buttons","Molecular Table Display", "Superposition","Annotate By Substructure","Customized Label 2D or 3D","Custom Rotation", "Copy Cut and Paste Row","Cut Vertical Alignment Block","Defective graphics on a laptop or Windows computer with a low end graphics card.", "Is it possible to draw dashed lines between atoms without displaying the corresponding bond length. I would like to do this to show which atoms are", "Searching the PDB","How to Read in a PDB File","Search and Align","How to make a local database.", "Molcart","Enumerate by Scaffold","Ligand Considerations","Database File Format", "Run VLS in the Graphical User Interface","Database File Format","Search and Align", "How can I download the MolCart vendor compounds provided by MolSoft?","How to decompose a library based on a Markush structure.", "Enumerate by Scaffold","R-Group Decomposition","R-Group Decomposition","How to Move Windows", "Delete","Delete","Protect Shell Objects From Deletion","I would like to delete all the residues in my protein except for the ones surrounding the ligand binding pocket.", "Deleting Columns and Rows","Undisplay Label","Delete All","Delete Label","Deleting Columns and Rows", "Delete Label","Undisplay Label","Deleting Columns and Rows","Delete","Edit Structure", "Delete All","Get Electron Density Map","Contour Electron Density Map","Convert Xray Density to Grid", "How do I load an electron density map into ICM?","How can I contour an electron density map and adjust contour levels and color?", "Occlusion Shading","Can you suggest some ways to remove a selection completely?", "How can I calculate the RMSD between two protein structures?","Insert a Dialog Box", "Insert a Dialog Box","Light Tab","Dihedral Angle","Label Variables","How can I display the dihedral angle?", "I have a small molecule which already has the 3D coordinates defined. How can I load the molecule and not optimize it so as to preserve the assigned 3D coordinates?", "Directories Preferences","Preferences","Defective graphics on a laptop or Windows computer with a low end graphics card.", "How to use the ICM Workspace Panel","How to Arrange Windows","How to Display Hydrogen Bonds Between a Ligand and Receptor.", "Preferences","Graphic Layers","Display Clash","Chemical Display","Generate Stereoismers", "How do I specify a particular color for only the carbon atoms of a molecules?","I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "What does as_graph mean?","I have the XYZ origin cross displayed - How can I undisplay this?", "The front and back part of my structure have been clipped away how do I restore these regions in my display.", "How can I display more information regarding an atom such as mmff type and charge?", "How can I display a structure in many different representations simultaneously?", "What is an iSee File?","How to check on the display status of an object in the command line.", "How do I display the distance between two atoms?","How do I display only the residues that surround the ligand binding pocket?", "How do I display weak hydrogen bonds?","How can I change the layout of a chemical table?", "Making Graphical Selections","Displaying only the residues that surround the ligand binding pocket.", "Displaying hydrogen bonds between a ligand and receptor.","Chemical Display","Delete Label", "Display Dihedral Angle","Displaying Distance Restraints","Display Distance Between Two Atoms - the quick way", "Display Gradient","Display and Undisplay Hydrogens","Meshes and Macroshape","Display Planar Angle", "How to Display a Molecule","Display Tab","How can I change the color of a grob atom based surface according to the underlying atom coloring scheme?", "Displaying Tethers","Display Rainbow, Box, Ruler","CPK Representation","Display Planar Angle", "Molecular Table Display","Display Dihedral Angle","Displaying Distances","Display Distance Between Two Atoms - the quick way", "Displaying Distance Restraints","Electrostatic potential","Display Gradient","Display and Undisplay Hydrogens", "Display and Undisplay Hydrogens","Macroshape","Meshes and Macroshape","Meshes Tab", "Display and Convert Molecule","(Un)display Origin","Electrostatic potential","Display Tab", "Structure Representation","Displaying Distance Restraints","Ribbon Representation", "Skin Representation","How to check on the display status of an object in the command line.", "Surface Representation","Surfaces","Meshes Tab","Molecular Table Display","Displaying Tethers", "Wire Representation","Stick and Ball (Xstick) Representation","How to Measure the Distance Between Two Atoms.", "Distance","Distance","Displaying Distances","Compare Two Sets","Is it possible to draw dashed lines between atoms without displaying the corresponding bond length. I would like to do this to show which atoms are", "Can you give me some tips on which options to use for RMSD calcu","How do I display the distance between two atoms?", "How do I display the distance between two atoms?","Font Preferences","Labels Tab", "Making a disulfide bond.","Data Clustering","Docking","Small Molecule Docking","Ligand Considerations", "ICM X-Ray AutoFit - Automated Model Building into Density","How do I sample conformations of flexible rings in docked ligands, for example, a \"chair-boat\" transition?", "How can I guide my docking to a known conformation of a smilar ligand?","How do I reload a docking project?", "In a VLS run how many times should I run the docking?","Some compounds are missing from my HITLIST.", "What constitutes a good docking score?","How do I identify the binding pockets in my receptor?", "How long does it take to dock one ligand using ICM-VLS?","What does thoroughness mean?", "When I setup the receptor I am asked to move a probe - what is this?","I want to dock to the receptor and include other molecules in the receptor such as a tightly bound water molecule - how can I do this?", "How can I run docking with a flexible receptor?","How can I run the docking simulation from the UNIX command line?", "I am docking a racemic compound how can I sample both R andS states during docking?", "Virtual Ligand Screening to Ricin Receptor","Virtual Ligand Screening to Cyclooxygenase", "Multiple Receptor Conformation Ensemble Docking Example","How can I run the docking simulation from the UNIX command line?", "How to Convert a Protein into an ICM Object","Protein Interface by ODA","Protein Interface by ODA", "Docking","Setting up the Docking Project","Reload a Docking Project","Flexible Receptor Docking and Multiple Receptor Conformations", "Fully Flexible Ligand and Receptor Docking","Multiple Receptor Conformation Docking", "Virtual Ligand Screening","Virtual Ligand Screening","VLS Getting Started","Run VLS in the Graphical User Interface", "Protein-Protein Docking","Protein-Protein Docking","Optimal Docking Area","Optimal Docking Area", "Protein-Protein Docking Procedure","Protein-Protein Docking Procedure","Protein-Protein Set Project", "Protein-Protein Receptor Setup","Protein-Protein Ligand Setup","Protein-Protein Make Receptor Maps", "Protein-Protein Docking Batch","Display Grid Docking Results","FAQ-Docking","What are the units of the energy values displayed after docking?", "When I view my docking run my ligand never jumps into the box - what did I do wrong?", "I have a complex I wish to generate an ICM VLS Score for, however I did not dock it using VLS. How can I do this?", "Why is there always a small difference between the score calculated interactively by scanScoreExternal and that obtained by docking (VLS)?", "Docking Examples","Re-Dock Biotin to the Streptavidin Receptor","Re-Dock an Inhibitor to Ricin Crystal Structure", "Docking a Markush Library","Setting up the Docking Project","Template Docking","Review and adjust binding site", "Review and adjust binding site","How do I monitor and terminate a background docking job?", "Batch Docking","Review and adjust binding site","How do I sample flexible ring conformations (boat, chair etc..) during docking?", "How do I sample flexible ring conformations (boat, chair etc..) during docking?", "Make a HIT LIST - Only available with ICM-VLS","Interactive Docking","(Re)Make Receptor Maps", "Setting up the Docking Project","Begin the Docking Simulation","Set Project Name", "Make a HIT LIST - Only available with ICM-VLS","Setup Receptor","Viewing Your Docking Results", "Results - Scan Hits","Docking Results - View Stack Conformations","Make a HIT LIST - Only available with ICM-VLS", "How do I sample flexible ring conformations (boat, chair etc..) during docking?", "Make a HIT LIST - Only available with ICM-VLS","Docking Results - View Stack Conformations", "Template Docking","HTML","Insert Script","Insert a Dialog Box","Document Navigation", "I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "How do I use the Dollar $ in ICM Scripts?","Property Monitor","Display Tab","Structure Representation", "General Preferences","How to remove chain breaks (dotted lines)","How to remove chain breaks (dotted lines)", "How to remove the dotted lines in chain breaks.","Editing structure using keyboard", "How can I download the MolCart vendor compounds provided by MolSoft?","How to Drag and Drop", "How to Make an Alignment using Drag and Drop","Font Preferences","Labeling Residues", "Drag and Drop","Insert Script","How can I merge two separate objects into one?", "Sequence Drag and Drop and the Alignment Editor","Drag and Drop","Drag Res Labels", "How to Drag and Drop","How to Access the ICM Molecular Editor","Isis Draw Copy and Paste", "Enumerate by Reaction","How can I draw small molecules?","Drawing a New Chemical Structure", "How to Drag and Drop","How to Make an Alignment using Drag and Drop","Drag and Drop", "Insert Script","How can I merge two separate objects into one?","Sequence Drag and Drop and the Alignment Editor", "Calculate Properties","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "What is considered a good druglikeness value?","Property Monitor","How to Display a Binding Pocket Surface", "How to Display a Binding Pocket Surface","Easy Rotate","How do I read in a small molecule from ISIS draw and convert it to 3D?", "Edit an Alignment","Editing a Chemical Structure","Edit Molecule","Edit Ligand", "Ligand-Editor-Preferences","Ligand Tools","Edit Menu","Editing a Molecular Document", "Molecular Editor","Edit Database","Edit a Movie","Selection","Edit Slide Description", "Editing a Table","How to edit a 3D pharmacophore.","Edit Molecule","Edit a Movie", "Edit Molecule","How to Access the ICM Molecular Editor","Pharmacophore","How do I show the sequence conservation around the ligand binding site?", "Displaying the sequence conservation around the ligand binding site.","PDB Search", "Get Electron Density Map","Contour Electron Density Map","Convert Xray Density to Grid", "Get Electron Density Map","Contour Electron Density Map","Convert Xray Density to Grid", "How do I load an electron density map into ICM?","How can I contour an electron density map and adjust contour levels and color?", "Map's Original Cell","Tools Menu - Xray","Load","Tools Menu - Xray","ICM X-Ray AutoFit - Automated Model Building into Density", "How to Display Electrostatic Surfaces Around a Ligand.","Electrostatic potential", "Protein-Protein Make Receptor Maps","Editing structure using keyboard","Embed in Web Browser", "How to Embed in Microsoft PowerPoint 2003","How to Embed in Microsoft PowerPoint 2007", "How to Change ActiveICM Component Properties","How to Change ActiveICM Component Properties", "ActiveICM","Embed in Web Browser","ActiveICM","Embed in Web Browser","ActiveICM", "Embed in Web Browser","ActiveICM","ActiveICM","How to Embed in Microsoft PowerPoint 2003", "How to Embed in Microsoft PowerPoint 2007","I am docking a racemic compound how can I sample both R andS states during docking?", "How to Convert a Protein into an ICM Object","Protein Health","Display Clash","Docking Results - View Stack Conformations", "I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "What are the units of the energy values displayed after docking?","I do not have ICM-VLS but I would like to calculate the binding energy of my docked complex - how can I do this?", "How do I view a stack of solutions after a simulations?","I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "Energy Terms","How to Generate Combinatorial Libraries","How to enumerate a chemical library by reaction.", "Enumerate by Scaffold","Saving Chemical Images","How do I change the tautomeric form of Histidine in a structure?", "MolCart installation error on 64Bit machines","MolCart installation error on 64Bit machines", "How do I turn off the annoying beep?","How to use the Graphics window controls", "Compare Two Sets","Export to Excel","Filter Search","Quit","Quit","Chemical View Options", "Fully Flexible Ligand and Receptor Docking","Fully Flexible Ligand and Receptor Docking", "Export Ramachandran Plot","Export to Excel","How to Extract a Sequence from a PDB Structure.", "Load Sequence","How do I show the sequence conservation around the ligand binding site?", "I have a small molecule displayed in 3D in a loaded PDB file. How can I extract this molecule into an ICM Chemical Table?", "Displaying the sequence conservation around the ligand binding site.","Extract from ICB", "Extract Sub-Alignment As Is","How to extract a 2D sketch of a ligand in complex with a PDB strcture.", "Extract from ICB","How to extract a 3D pharmacophore from a ligand.","Frequently Asked Questions", "FAQ Hardware","FAQ Graphics and Display","How can I select only the backbone atoms?", "FAQ Structure","FAQ-Docking","FAQ-Simulations","FAQ-Script","I am having problems with my ICM script when running from the unix command line.", "How do I read in a small molecule from ISIS draw and convert it to 3D?","When using ActiveICM is there a way to set a RELATIVE path to an icb file rath than ABSOLUTE?", "Is there a way to build a classification model using the APF output?","How do I set a formal charge?", "How can I display more information regarding an atom such as mmff type and charge?", "ICM and AutoSave","How can I select only the backbone atoms?","How to change the background color with one click?", "How do I monitor and terminate a background docking job?","How do I turn off the annoying beep?", "I do not have ICM-VLS but I would like to calculate the binding energy of my docked complex - how can I do this?", "How do I set a blend transition effect between two slides?","How to remove the dotted lines in chain breaks.", "How can I change the torsion angle?","How can I change the layout of a chemical table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "How do I perform a chemical search","FAQ-Cheminformatics","The front and back part of my structure have been clipped away how do I restore these regions in my display.", "How can I select the closest residue from the center of mass of a selected residue?", "How do I specify a particular color for only the carbon atoms of a molecules?","How can I change the color of a grob atom based surface according to the underlying atom coloring scheme?", "How to check on the display status of an object in the command line.","How do I change the bond types and add formal charges to a ligand from the PDB?", "How do I make a covalent bond between a ligand and a receptor?","I would like to delete all the residues in my protein except for the ones surrounding the ligand binding pocket.", "Can you suggest some ways to remove a selection completely?","How can I display the dihedral angle?", "When I setup the receptor I am asked to move a probe - what is this?","I am docking a racemic compound how can I sample both R andS states during docking?", "In a VLS run how many times should I run the docking?","FAQ-Docking","How long does it take to dock one ligand using ICM-VLS?", "How do I use the Dollar $ in ICM Scripts?","What is considered a good druglikeness value?", "What are the units of the energy values displayed after docking?","I have a small molecule displayed in 3D in a loaded PDB file. How can I extract this molecule into an ICM Chemical Table?", "How can I run docking with a flexible receptor?","How do I sample flexible ring conformations (boat, chair etc..) during docking?", "How to change font size in html-documents, alignments, terminal, table, graphics?", "Is there a way to determine the name of the current table displayed GUI?","ICM graphics crashes.", "FAQ Graphics and Display","How can I guide my docking to a known conformation of a smilar ligand?", "FAQ Hardware","Some compounds are missing from my HITLIST.","What is an iSee File?", "How do I identify the binding pockets in my receptor?","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "FAQ Installation","Is it possible to draw dashed lines between atoms without displaying the corresponding bond length. I would like to do this to show which atoms are", "When I view my docking run my ligand never jumps into the box - what did I do wrong?", "How can I merge two separate objects into one?","MolCart installation error on 64Bit machines", "How do I make a new molcart database from a query search?","I have a database in MolCart and I want to save it in SDF format - how can I do this?", "How do I perform a text query on a database in MolCart?","I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "How can I draw small molecules?","I would like to create a movie wherein I \"walk\" through the molecule by moving the front clipping plane to the end. Can I write a loop that moves the clipping and generates an image after every step to generate my movie afterwards?", "How can I write a script in the Graphical User Interface?","How do I read in all the structures in a PDB file of a protein solved by NMR?", "I downloaded and installed ICM. It seems to start fine. However it dies every time I try to open something, giving an NVIDIA error. NVIDIA: Could not open the device file /dev/nvidiactl (Permission denied).", "I have the XYZ origin cross displayed - How can I undisplay this?","Which score value should I use for analysis.", "How can I find out which residues are surrounding a ligand binding pocket?","I have a small molecule which already has the 3D coordinates defined. How can I load the molecule and not optimize it so as to preserve the assigned 3D coordinates?", "Does ICM support quad-buffer stereo?","I want to dock to the receptor and include other molecules in the receptor such as a tightly bound water molecule - how can I do this?", "How do I reload a docking project?","If I have multiple graphical selections how can I remove one without losing the others?", "How Do I renumber the residues in a PDB file","How do I sample conformations of flexible rings in docked ligands, for example, a \"chair-boat\" transition?", "How can I calculate the RMSD between two protein structures?","Can you give me some tips on which options to use for RMSD calcu", "How to rotate a 2D chemical sketch so it fits nicely in its cell in a chemical table?", "I have a complex I wish to generate an ICM VLS Score for, however I did not dock it using VLS. How can I do this?", "Why is there always a small difference between the score calculated interactively by scanScoreExternal and that obtained by docking (VLS)?", "What constitutes a good docking score?","FAQ-Script","SGI ICM installation problem", "FAQ-Simulations","How to convert SMILES strings to 2D","How do I write a script to calculate solvent-accessible surface and tabulate the results to show area for each residue in a protein?", "How do I make a disulfide bond?","FAQ Structure","How do I superimpose two proteins?", "What does thoroughness mean?","How to make a transparent ribbon?","How to truncate a mesh object?", "How do I view a stack of solutions after a simulations?","How do I display weak hydrogen bonds?", "How to write a pdb file?","How can I contour an electron density map and adjust contour levels and color?", "I want to visualize weak hydrogen bonds how can I change the H-bond cutoff parameter?", "How do I load an electron density map into ICM?","How do I color ribbon models according to Optimal Docking Area (ODA)", "Problem with stereo?","How to Work With Sequences and Alignments","How to Load a FASTA Format File", "Open","Loading Your PDB File","Close Project","Save Project Compatible with ICM 3_5", "Export as ActiceICM Html","Load","File Menu","Save with Password","Quick Image", "How to Save an ICM Project File","Recent Files","Restore Recent Backup","Browse Database", "How do I specify a particular color for only the carbon atoms of a molecules?","Filter Selection", "Filtering a Selection.","Find Related Chains","Chemical Find and Replace","Find Related Chains", "Dihedral Angle","Planar Angle","How do I perform a chemical search","How do I make a new molcart database from a query search?", "Rotate Chemical for Best-Fit","ICM X-Ray AutoFit - Automated Model Building into Density", "How can I run docking with a flexible receptor?","Least Squares Fitting","ICM X-Ray AutoFit - Automated Model Building into Density", "Flexible Substructure Superposition","Local Flexibility","Superposition","Flexible Receptor Docking and Multiple Receptor Conformations", "Flexible Receptor Docking and Multiple Receptor Conformations","Fully Flexible Ligand and Receptor Docking", "Multiple Receptor Conformation Docking","How can I run docking with a flexible receptor?", "Multiple Receptor Conformation Ensemble Docking Example","How do I sample conformations of flexible rings in docked ligands, for example, a \"chair-boat\" transition?", "Fog","Fog","Graphics and View Tools","Preferences","Font Preferences","Labeling Atoms", "Labeling Residues","Change Column Format","Tree View","Chemical View Options","Font Preferences", "Alignment Editor","How to change font size in html-documents, alignments, terminal, table, graphics?", "Molecule and Background Coloring","How to change the view of a chemical spreadsheet - form, table and grid.", "Table View (Grid Layout)","How to Convert a Chemical from the PDB","How do I set a formal charge?", "Reading a Table","Change Column Format","Property Monitor","Calculate Properties", "Color Chemical Structure","R-Group Decomposition","Generating Chemical Fragments", "Generating Chemical Fragments","Six Frame Translation","Color Chemical Structure", "Mesh Clipping","Mesh Clipping","Full Scene Antialias","Full Screen","Full Screen", "Inserting Columns","Column Statistics","Annotate By Substructure","General Preferences", "Selection Tools","Biomolecule Generator","Generate 3D Conformers","Stereo Hardware Questions", "Which stereo glasses?","Problem with stereo?","Optimize H, His, Asn, Gln and Pro", "Optimize H,His,Asn,Gln,Pro","Load","Google 3D Objects (Sketchup)","Meshes Tab","Google 3D Objects (Sketchup)", "Introduction","How do I specify a particular color for only the carbon atoms of a molecules?", "Converting a Chemical from the PDB using the ICM Workspace","How to Convert a Chemical from the PDB using the Graphical Display", "Converting a Chemical from the PDB using the ICM Workspace","Converting a Chemical from the PDB using the Graphical Display", "FAQ Graphics and Display","Coloring and Changing Molecule Representations","I downloaded and installed ICM. It seems to start fine. However it dies every time I try to open something, giving an NVIDIA error. NVIDIA: Could not open the device file /dev/nvidiactl (Permission denied).", "Graphics and View Tools","Graphics and View Tools","Defective graphics on a laptop or Windows computer with a low end graphics card.", "Graphics Preferences","How to use the Graphics window controls","How to use the Graphics window controls", "Shadows","How to change the view of a chemical spreadsheet - form, table and grid.", "Molecular Table Display","Superposition","How can I change the layout of a chemical table?", "Multiple Receptor Conformation Ensemble Docking Example","General Preferences","Get Electron Density Map", "Contour Electron Density Map","Convert Xray Density to Grid","R-Group Decomposition", "Find Best Replacement Group","Generating Chemical Fragments","Calculate Properties", "Standardize Table","GUI Preferences","Menu Options","GUI Preferences","Tabs","How can I guide my docking to a known conformation of a smilar ligand?", "I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "How to Display Hydrogen Bonds Between a Ligand and Receptor.","Is it possible to draw dashed lines between atoms without displaying the corresponding bond length. I would like to do this to show which atoms are", "I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "Displaying hydrogen bonds between a ligand and receptor.","FAQ Hardware","Hardware Stereo", "I want to visualize weak hydrogen bonds how can I change the H-bond cutoff parameter?", "I want to visualize weak hydrogen bonds how can I change the H-bond cutoff parameter?", "Display PDB Header","Add a title to a plot","Protein Health","Protein Health","Assign Helices and Strands", "How do I color a structure by secondary structure?","Chemical View Options","Alignment Gaps", "Alignment Gaps","Hide and Show Columns","Write Image","High Quality","Optimize H, His, Asn, Gln and Pro", "How do I change the tautomeric form of Histidine in a structure?","Optimize H,His,Asn,Gln,Pro", "How do I change the tautomeric form of Histidine in a structure?","How do I change the tautomeric form of Histidine in a structure?", "How to Generate Plots and Histograms","How to make a histogram.","Plotting Table Data", "Column Histogram","Add a title to a plot","Change Axis Data","Change Mark Shape or Size", "Change Mark Color","Grid and Axis Display","Least Squares Fitting","Zoom, Translate and Center", "Plot Selection","Print Plot","Table Inline Plots","How to Plot Histograms and Scatterplots of VLS Data", "To construct a histogram of your VLS data","Histogram Bins","Histogram Options", "Histogram Options","Histogram Bins","Histogram Options","Histogram Options","Histogram Options", "Histogram Options","Viewing Your Docking Results","Make a HIT LIST - Only available with ICM-VLS", "VLS Results","Sorting the compounds in your HITLIST","To construct a histogram of your VLS data", "Some compounds are missing from my HITLIST.","Find Related Chains","Homology Menu and Modelling Tools", "Homology Modeling Introduction","Getting Started","Making an interactive model.", "Loop Modeling","Regularization","Homology Modeling and Structure Analysis Tools", "Homology Modeling","Display Loops","Homology Modeling Introduction","Getting Started", "How to search a 2D pharmacophore.","How to Work with the ICM 3D Ligand Editor","How to add and sample new substiutents to your ligand in the ICM 3D Ligand Editor.", "How to begin editing your ligand in the ICM 3D Ligand Editor.","How to center on a ligand in the ICM 3D Ligand Editor.", "How to configure the default display in the ICM 3D Ligand Editor.","How to re-dock a ligand in the ICM 3D Ligand Editor.", "How to restrain (tether) atoms during docking.","How to edit the ligand in 2D in the ICM 3D Ligand Editor.", "How to display energy atomic circles in the ICM 3D Ligand Editor.","How to display and undisplay hydrogen atoms in the ICM 3D Ligand Editor.", "How to sample linkers between two chemical fragments.","How to display hydrogen bonds in the ICM 3D ligand editor.", "How to perform ligand minimization in the ICM 3D Ligand Editor.","How to sample more than one substituent at a time in the ICM 3D Ligand Editor.", "How to change the 3D Ligand Editor preferences.","How to change the size of the ligand binding pocket - change purple box size.", "How to add an edited ligand to a chemical spreadsheet (table).","How to screen databases of chemical substituents.", "How to setup the ligand in the ICM 3D Ligand Editor.","How to setup the receptor in the ICM 3D Ligand Editor.", "How to display and undisplay the ligand surface representation in the ICM 3D Ligand Editor.", "How to undo and redo changes in the ICM 3D Ligand Editor.","How to display unsatisfied hydrogen bonds in the ICM 3D Ligand Editor.", "How to add columns into a chemical spreadsheet.","How to change the view of a chemical spreadsheet - form, table and grid.", "How to Convert Chemicals from 2D to 3D","How to generate 3D ligand conformers.", "How to convert 2D chemical sketches to 3D.","How to convert 2D sketches in the molecule editor into 3D.", "How to Perform Chemical Clustering","How to setup a chemical search.","How to Superimpose Chemicals", "How to use Atomic Property Fields for Chemical Superposition","How to Perform Rigid and Flexible Chemical Substructure Superposition.", "How to select representative centers from a tree.","How to color a 2D chemical sketch by pharmacophore feature.", "How to copy and paste 2D chemicals.","How to copy, cut and paste columns and rows in a chemical spreadsheet.", "How to decompose a library based on a Markush structure.","How to identify duplicate chemicals in a chemical spreadsheet.", "How to edit a 3D pharmacophore.","How to edit data inside a chemical spreadsheet.", "How to edit the tree - labels, spacing and coloring.","How to Generate Combinatorial Libraries", "How to export your chemical spreadsheet into Excel.","How to extract a 2D sketch of a ligand in complex with a PDB strcture.", "How to extract a 3D pharmacophore from a ligand.","How to filter columns in a chemical spreadsheet.", "How to use find and replace in a chemical spreadsheet.","How to make a histogram.", "How to Access the ICM Molecular Editor","How to Import, Sketch, and Edit Chemicals", "How to load a mol, sdf or mol2 file.","How to mark and label rows in a chemical spreadsheet.", "How to enumerate a Markush library.","How to create a Markush structure.","How to merge two chemical spreadsheets.", "How to Work with Pharmacophores","How to make an X-Y scatter plot.","How to Generate Plots and Histograms", "How to calculate chemical properties in a chemical spreadsheet.","How to Build and Apply QSAR Prediction Models", "How to build a QSAR prediction model.","How to apply a QSAR prediction model.","How to enumerate a chemical library by reaction.", "How to reorder branches and change the distance of trees.","How to save a 2D sketch in mol format.", "How to save a chemical spreadsheet in sdf format.","How to search chemical spreadsheets, local databases and MolCart.", "How to send a 3D pharmacophore search query.","How to add conditions to your chemical search.", "How to draw a chemical search query.","How to send a chemical search query.","How to show and hide columns and rows in a chemical spreadsheet.", "How to sketch chemicals in the ICM Molecular Editor.","How to save a 2D sketch into a chemical spreadsheet.", "How to use SMILES strings to sketch a chemical.","How to sort a column(s) in a chemical spreadsheet.", "How to remove salts, explicit hydrogens and standardize chemical groups.","How to Generate Stereoisomers and Tautomers", "How to insert hyperlinks to the PDB, PubMed, and Uniprot.","How to print a chemical spreadsheet.", "How to Perform Chemical Searching.","How to perform chemical clustering.","How to Work With Chemical Spreadsheets", "How to Use the Graphical Display","How to generate stereoisomers.","How to generate tautomers.", "I want to visualize weak hydrogen bonds how can I change the H-bond cutoff parameter?", "HTML","HTML","Export as ActiceICM Html","Creating a Molecular Document","Editing a Molecular Document", "Document Navigation","How to change font size in html-documents, alignments, terminal, table, graphics?", "Right Click Options","Query Setup","How to Convert a Protein into an ICM Object", "How to Display Hydrogen Bonds Between a Ligand and Receptor.","Hydrogen Bonding", "Optimize H, His, Asn, Gln and Pro","Right Click Options","Query Setup","Is it possible to draw dashed lines between atoms without displaying the corresponding bond length. I would like to do this to show which atoms are", "I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Displaying hydrogen bonds between a ligand and receptor.","Hydrogen Bonding","Property Monitor", "How do I display weak hydrogen bonds?","Chemical View Options","Chemical View Options", "How to remove salts, explicit hydrogens and standardize chemical groups.","Creating a Molecular Document", "Editing a Molecular Document","How to Save an ICM Project File","How to Make a Molecular Document", "HTML","Extract from ICB","Export as ActiceICM Html","I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "What is an iSee File?","How do I set a blend transition effect between two slides?", "When using ActiveICM is there a way to set a RELATIVE path to an icb file rath than ABSOLUTE?", "How to Make a Molecular Document","What is an iSee File?","When using ActiveICM is there a way to set a RELATIVE path to an icb file rath than ABSOLUTE?", "When using ActiveICM is there a way to set a RELATIVE path to an icb file rath than ABSOLUTE?", "ICM crashes, or hangs if you are trying to start the Chemical Editor, or a Query window", "How to Save ICM Projects","ICM crashes, or hangs if you are trying to start the Chemical Editor, or a Query window", "Search and Align","icmPocketFinder","How can I find out which residues are surrounding a ligand binding pocket?", "How do I identify the binding pockets in my receptor?","How to Make a Picture","Preferences", "General Preferences","Saving a Plot Image","Saving Chemical Structures and Images", "Saving Chemical Images","Insert Image","Image Preferences","Load","High Quality", "Quick Image","Does ICM support quad-buffer stereo?","How do I perform a text query on a database in MolCart?", "How can I run docking with a flexible receptor?","Flexible Receptor Docking and Multiple Receptor Conformations", "Fully Flexible Ligand and Receptor Docking","Multiple Receptor Conformation Ensemble Docking Example", "Insert Script","Inserting Columns","Insert Image","Inserting Rows","Insert Script", "Introduction","Molcart Installation","MolCart installation error on 64Bit machines", "Where do I save my MolCart license?","FAQ Installation","SGI ICM installation problem", "I do not have ICM-VLS but I would like to calculate the binding energy of my docked complex - how can I do this?", "Contact Areas","Is it possible to draw dashed lines between atoms without displaying the corresponding bond length. I would like to do this to show which atoms are", "Interactive Docking","Interactive Loop Modeling","Making an interactive model.", "Interactive Modeling","Making an interactive model.","Interactive Modeling","Introduction", "Interrupt Animation","Interrupt Animation","Introduction","Making Table Selections", "Defective graphics on a laptop or Windows computer with a low end graphics card.", "Insert a Dialog Box","Isis Draw Copy and Paste","Isis Draw Copy and Paste","Right Click Options", "Query Setup","IUPAC Chemical Nomenclature","How do I monitor and terminate a background docking job?", "Running VLS Jobs in PBS UNIX Cluster Environment","Merge Two Sets","Cluster","Editing structure using keyboard", "Keyboard and Mouse Shortcuts","Editing structure using keyboard","Meshes Tab","Google 3D Objects (Sketchup)", "How to Measure the Distance Between Two Atoms.","Font Preferences","Tree View","How can I display more information regarding an atom such as mmff type and charge?", "Labeling and Annotation","Label Residues","Label Atoms","2D and 3D Labels","Label Annotation", "Labeling Atoms","Changing Label Colors","Move Residue Label","Labeling Residues", "Labeling Sites","Label Variables","Labels Tab","Labeling","Labels Tab","Label Annotation", "Labeling","Labeling Atoms","Changing Label Colors","Customized Label 2D or 3D","Labeling", "Undisplay Label","Displaying Distances","Drag Res Labels","Drag Res Labels","Move Residue Label", "Labeling","Labeling Residues","Labeling","Labeling Sites","Labeling","Label Variables", "How can I display the dihedral angle?","Labeling","Chemical View Options","Displaying Distances", "Labels Tab","Image Preferences","Making Basic Selections","Making Sequence Selections in the ICM Workspace", "Graphic Layers","Graphic Layers","Learn and Predict","Learn","Build Prediction Model", "Predict","Is there a way to build a classification model using the APF output?", "Learn and Predict","A little theory on learning","Least Squares Fitting","Enumerate by Scaffold", "How to enumerate a chemical library by reaction.","Where do I save my MolCart license?", "Ligand Considerations","Flexible Receptor Docking and Multiple Receptor Conformations", "Protein-Protein Ligand Setup","Epitope Selection","How can I merge two separate objects into one?", "How do I display only the residues that surround the ligand binding pocket?","I do not have ICM-VLS but I would like to calculate the binding energy of my docked complex - how can I do this?", "When I view my docking run my ligand never jumps into the box - what did I do wrong?", "I have a small molecule displayed in 3D in a loaded PDB file. How can I extract this molecule into an ICM Chemical Table?", "Displaying only the residues that surround the ligand binding pocket.","Find Best Replacement Group", "How To Use The Ligand Editor","Ligand Editor Preferences","Insert a linker","How do I display only the residues that surround the ligand binding pocket?", "Impose Restraint (tethers) To Ligand Atoms","ICM Convert","How To Use The Ligand Editor", "Setup Ligand and Receptor","Insert a linker","Re-Dock and Minimize Ligand","Pocket Display Options", "Edit Ligand","Pocket Display Options","Pocket Display Options","Pocket Display Options", "Ligand-Editor-Preferences","Impose Restraint (tethers) To Ligand Atoms","Pocket Display Options", "Impose Restraint (tethers) To Ligand Atoms","Docking a Markush Library","How to Display a Binding Pocket Surface", "Contact Areas","How to display and undisplay the ligand surface representation in the ICM 3D Ligand Editor.", "Light Tab","Light Tab","Calculate Properties","What is considered a good druglikeness value?", "General Preferences","Tree View","Is it possible to draw dashed lines between atoms without displaying the corresponding bond length. I would like to do this to show which atoms are", "Graphics Preferences","Link to Structure","Ligand Binding Pocket Analysis Examples", "Insert a linker","Making Links","Making Links","Molcart Installation","How to Work With Sequences and Alignments", "How to Load a FASTA Format File","Open","Recent Files","Get Electron Density Map", "Contour Electron Density Map","Convert Xray Density to Grid","Loading Your PDB File", "Load Sequence","Get Electron Density Map","Load Example Alignment","Loading Your PDB File", "Load Sequence","MMFF","PDB Search Results Table","How to Download a SwissProt sequence", "I would like to have a local copy of the PDB - any advice?","I would like to have a local copy of the NCBI Blast database- any advice?", "Working with Local Databases","Local Flexibility","Browse Database","Edit Database", "Query Local Database","Edit Database","I would like to have a local copy of the PDB - any advice?", "I would like to have a local copy of the NCBI Blast database- any advice?","Mesh Clipping", "Mesh Clipping","Set Chemical Table 3D Browse Mode","Change Axis Data","Property Monitor", "Calculate Properties","Property Monitor","Calculate Properties","Change Axis Data", "Quit","Loop Modeling","How do I color a structure by secondary structure?","Loop Modeling", "Interactive Loop Modeling","Sample Loop","Sample Loop","Sample Loop","Molcart Installation", "Advanced use of activeICM: Macros to direct visualisation changes","Macro Shape", "Macroshape","Constructing a New Peptide","New Table","Generate New Table","Make Animation", "Make Animation","How to rotate a 2D chemical sketch so it fits nicely in its cell in a chemical table?", "Making Molecular Documents","How to make a local database.","View-Defined Movie Making", "(Re)Make Receptor Maps","Making Selections","Constructing New DNA or RNA","Constructing New DNA or RNA", "How do I make a covalent bond between a ligand and a receptor?","Constructing a New Compound", "Constructing a New Compound","Making a disulfide bond.","How do I make a disulfide bond?", "New","New","Constructing New Protein and Nucleic Acid Sequences","Making Molecular Slides", "Making Molecular Documents","Change Mark Color","Font Preferences","Get Electron Density Map", "Contour Electron Density Map","Convert Xray Density to Grid","Map's Original Cell", "Protein-Protein Make Receptor Maps","How do I load an electron density map into ICM?", "How can I contour an electron density map and adjust contour levels and color?", "When I view my docking run my ligand never jumps into the box - what did I do wrong?", "Multiple Receptor Conformation Ensemble Docking Example","Map's Original Cell","Mark and Select Rows", "Mark and Select Rows","Change Mark Shape or Size","Change Mark Shape or Size","Create/Modify Markush", "R-Group Decomposition","Docking a Markush Library","Docking a Markush Library","How to enumerate a Markush library.", "How can I select the closest residue from the center of mass of a selected residue?", "Meshes Tab","Cluster","Shell Preferences","How can I calculate the RMSD between two protein structures?", "Insert a Dialog Box","Chemistry Menu","Docking Menu","Homology Menu","MolMechanics Menu", "Tools Menu - Chemical Search","Tools Menu - Molecular Editor","Windows Menu","Merge Two Sets", "How can I merge two separate objects into one?","Merge Two Sets","How to Display the Residues Surrounding the Ligand Binding Pocket.", "How to Display Electrostatic Surfaces Around a Ligand.","Get Electron Density Map", "Contour Electron Density Map","Convert Xray Density to Grid","Mesh Clipping","Move and Resize Mesh", "Mesh Clipping","Occlusion Shading","I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "Mesh Clipping","Mesh Options.","Mesh Options.","Meshes Tab","Cluster","Minimize", "Minimize","Minimize","MMFF","How can I display more information regarding an atom such as mmff type and charge?", "How can I convert a chemical in a chemical table into 3D?","Labeling Atoms","Shell Preferences", "Homology Menu and Modelling Tools","Homology Modeling Introduction","Getting Started", "Build Model","Loop Modeling","Regularization","Homology Modeling and Structure Analysis Tools", "Homology Modeling","Display Loops","Modeler's View","Modeler's View","Regularization", "Interactive Modeling","How to Import, Sketch, and Edit Chemicals","Saving Chemical Structures and Images", "Saving from a chemical table.","Saving in the Molecular Editor","Saving in the ICM Workspace", "Saving Chemical Images","Virtual Ligand Screening to Cyclooxygenase","Virtual Ligand Screening to Cyclooxygenase", "How to Import, Sketch, and Edit Chemicals","Saving Chemical Structures and Images", "Saving from a chemical table.","Saving in the Molecular Editor","Saving in the ICM Workspace", "Saving Chemical Images","Working with Local Databases","Molcart","Molcart","Molcart Installation", "Molcart Getting Started","Molcart Search","Molcart Administration","MolCart installation error on 64Bit machines", "FAQ-Cheminformatics","How can I download the MolCart vendor compounds provided by MolSoft?", "I have a database in MolCart and I want to save it in SDF format - how can I do this?", "How do I perform a chemical search","How do I make a new molcart database from a query search?", "How do I perform a text query on a database in MolCart?","Molcart Administration", "How do I connect to Molcart?","How can I download the MolCart vendor compounds provided by MolSoft?", "How do I generate the hostid for my MolCart license?","Molcart Installation","Where do I save my MolCart license?", "Molcart Search","Molcart Getting Started","How do I connect to Molcart?","How do I generate the hostid for my MolCart license?", "How do I generate the hostid for my MolCart license?","Where do I save my MolCart license?", "How to Access the ICM Molecular Editor","Zoom, Translate and Z-rotate a Chemical in a table.", "Set Chemical Table 3D Browse Mode","Rotate Chemical for Best-Fit","Color Chemical Structure", "Generate 3D Conformers","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Making Molecular Animations, Slides, and Documents","Molecular Animations and Transitions", "HTML","How can I draw small molecules?","Copy, Cut and Paste","Copy, Cut and Paste", "Copy, Cut and Paste","Undo and Redo","Molecular Editor Selections","Undo and Redo", "Homology Menu and Modelling Tools","How to Make a Molecular Document","How to Incorporate Transition Effects Between Slides", "2D Depiction","Property Monitor","How to Access the ICM Molecular Editor","What does as_graph mean?", "How do I read in a small molecule from ISIS draw and convert it to 3D?","How to Import, Sketch, and Edit Chemicals", "Molecular Editor","Find Related Chains","Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "ICM Convert","Optimize H, His, Asn, Gln and Pro","How do I view a stack of solutions after a simulations?", "Edit Structure","Optimize H,His,Asn,Gln,Pro","Minimize","MMFF","Regularization", "Sample Loop","Energy Terms","Stack","Minimize","MMFF","Working with Local Databases", "Query Local Database","I do not see the chemical property monitor in the molecular editor. Where is it?", "Chemical View Options","Making an amino acid mutation","How do I make a movie of my montecarlo simulation and write all output.", "How to Move a Structure in the Graphical Display","Keyboard and Mouse Shortcuts", "Move Buttons","Movie Making","Movie Making Options","Screen-grabbing Movie","How to Drag and Drop", "How to Move Windows","Save Viewpoint","Move Buttons","Connect (Move)","Move and Resize Mesh", "How can I merge two separate objects into one?","Move and Resize Mesh","Move Slide", "Move Slide","Move Buttons","Graphics and View Tools","Keyboard and Mouse Shortcuts", "Keyboard and Mouse Shortcuts","Keyboard and Mouse Shortcuts","Keyboard and Mouse Shortcuts", "Keyboard and Mouse Shortcuts","Movie Tab","Screen-grabbing Movie","View-Defined Movie Making", "I would like to create a movie wherein I \"walk\" through the molecule by moving the front clipping plane to the end. Can I write a loop that moves the clipping and generates an image after every step to generate my movie afterwards?", "How do I make a movie of my montecarlo simulation and write all output.","Movie Files and Resolution Setup", "How do I make a movie of my montecarlo simulation and write all output.","Defining a Movie Scene", "Movie Tab","Movie Files and Resolution Setup","Edit a Movie","Preview and Export", "Movie Making","Movie Making Options","Movie Making","Movie Making Options","Screen-grabbing Movie", "Preview and Export","Movie Files and Resolution Setup","Rock","Rotate","Defining a Movie Scene", "Still","Tween","Movie Making","Movie Making Options","Screen-grabbing Movie","Movie Making", "Movie Making Options","Multiple APF Alignment of Compounds in a Table","Multiple Receptor Conformation Docking", "Multiple Receptor Conformation Ensemble Docking Example","Multiple Receptor Conformation Docking", "I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "How do I mutate a residue?","How do I mutate a terminal N or C residue?","How do I change the tautomeric form of Histidine in a structure?", "How do I mutate a residue?","How do I mutate a terminal N or C residue?","Making an amino acid mutation", "How do I mutate a residue?","How do I mutate a terminal N or C residue?","Edit Slide Description", "Workspace Navigation","How can I select the closest residue from the center of mass of a selected residue?", "Making a Spherical Selection.","How to Work With Sequences and Alignments","How to Make a New Sequence", "How to Access the ICM Molecular Editor","Constructing a New Peptide","Load Sequence", "Constructing a New Compound","Constructing New DNA or RNA","Constructing a New Peptide", "Constructing New Protein and Nucleic Acid Sequences","Generate New Table","Constructing a New Compound", "Constructing a New Compound","Constructing New DNA or RNA","Constructing New Protein and Nucleic Acid Sequences", "Constructing New DNA or RNA","Writing a Script in GUI.","New Table","Generate New Table", "How do I read in all the structures in a PDB file of a protein solved by NMR?","Introduction", "Chemical View Options","I downloaded and installed ICM. It seems to start fine. However it dies every time I try to open something, giving an NVIDIA error. NVIDIA: Could not open the device file /dev/nvidiactl (Permission denied).", "How to Drag and Drop","How to Convert a Protein into an ICM Object","Reloading a Saved ICM Object when ICM is Running", "Reloading a Saved ICM Object in Windows when ICM is not Running","What does as_graph mean?", "Working with PDB Structures","Converting PDB Files Into ICM Objects","Occlusion Shading", "Occlusion Shading","PDB Preparation - Occupancy and B-Factors","Protein Interface by ODA", "Protein-Protein Docking","Optimal Docking Area","Optimal Docking Area","Protein-Protein Docking Procedure", "Save Project Compatible with ICM 3_5","Label Variables","How can I display the dihedral angle?", "Open","Open","Open","Reading a Table","Open with Password","How to load a mol, sdf or mol2 file.", "How to load a mol, sdf or mol2 file.","How to load a mol, sdf or mol2 file.","Movie Making", "Movie Making Options","Open with Password","How to load a mol, sdf or mol2 file.", "Optimize H, His, Asn, Gln and Pro","Protein Interface by ODA","Protein-Protein Docking", "Optimal Docking Area","Protein-Protein Docking Procedure","Optimize H,His,Asn,Gln,Pro", "Optimize H, His, Asn, Gln and Pro","Making an amino acid mutation","(Un)display Origin", "I have the XYZ origin cross displayed - How can I undisplay this?","Alignment and Table Selections", "When I view my docking run my ligand never jumps into the box - what did I do wrong?", "I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "How do I superimpose two proteins?","How to Change ActiveICM Component Properties", "Crystallographic Neighbor","Pairwise Alignments","Parallelization","Parallelization", "Molcart Administration","Copy Cut and Paste Row","Isis Draw Copy and Paste","Running VLS Jobs in PBS UNIX Cluster Environment", "Principal Component Analysis","How to Extract a Sequence from a PDB Structure.", "How to: Protein Structure","How to Read in a PDB File","How to Convert a Protein into an ICM Object", "How to Convert a Chemical from the PDB","Load","Searching the PDB","Converting a Chemical from the PDB", "I would like to have a local copy of the PDB - any advice?","I would like to have a local copy of the NCBI Blast database- any advice?", "How Do I renumber the residues in a PDB file","Working with PDB Structures","Converting a Chemical from the PDB using the Graphical Display", "Converting a Chemical from the PDB using the ICM Workspace","How to write a pdb file?", "Display PDB Header","Sensitive PDB Similarity Searches","ICM Convert","Recent PDB Codes", "How to load a PDB Structure","PDB Search Tab","PDB Search Results Table","PDB Search Results Table", "PDB Search by Field","PDB Search by Homology","PDB Search by Identity","PDB Search Results Table", "PDB Search with External Seqeuence","Constructing a New Peptide","Perspective","Perspective", "Pharmacophore Drawing and Searching","Pharmacophore Draw 2D","Pharmacophore Draw 3D", "Pharmacophore Search","How to color a 2D chemical sketch by pharmacophore feature.", "Color Chemical Structure","Pharmacophore","Pharmacophore","2D Pharmacophore Searching", "3D Pharmacophore Searching","Pharmacophore Draw 3D","Pharmacophore Draw 2D","Pharmacophore Draw 3D", "Pharmacophore Draw 2D","Pharmacophore Draw 3D","Pharmacophore Draw 3D","Pharmacophore Draw 3D", "Pharmacophore Drawing and Searching","Pharmacophore Search","3D Pharmacophore Searching", "2D Pharmacophore Searching","How to search a 2D pharmacophore.","Label Variables", "How can I display the dihedral angle?","Phylogenetic Trees","Phylogenetic Trees", "Making Basic Selections","Making Sequence Selections in the ICM Workspace","Graphics and View Tools", "How to use the Graphics window controls","How to use the Graphics window controls", "How to Make a Picture","Quick Image","Insert Image","How to Make a Picture","Planar Angle", "Label Variables","How can I display the dihedral angle?","Display Planar Angle", "Clipping Tools","Mesh Clipping","Mesh Clipping","Graphic Layers","Mesh Clipping", "The front and back part of my structure have been clipped away how do I restore these regions in my display.", "I would like to create a movie wherein I \"walk\" through the molecule by moving the front clipping plane to the end. Can I write a loop that moves the clipping and generates an image after every step to generate my movie afterwards?", "How can I display a structure in many different representations simultaneously?", "How can I display a structure in many different representations simultaneously?", "How to Generate Plots and Histograms","How to make an X-Y scatter plot.","Preferences", "Plot Preferences","Plotting Table Data","Column Histogram","Plotting two columns", "Plotting two columns","Add a title to a plot","Change Axis Data","Change Mark Shape or Size", "Change Mark Color","Grid and Axis Display","Least Squares Fitting","Zoom, Translate and Center", "Plot Selection","Print Plot","Saving a Plot Image","Table Inline Plots","How to Plot Histograms and Scatterplots of VLS Data", "Change Axis Data","Change Mark Color","Tools Menu - Extras","Plot Function","Grid and Axis Display", "Add a title to a plot","Table Inline Plots","Logarithmic Plots","Change Mark Shape or Size", "Plot Preferences","Least Squares Fitting","Plot Selection","Zoom, Translate and Center", "Grid and Axis Display","Grid and Axis Display","Grid and Axis Display","Table Inline Plots", "Logarithmic Plots","Learn and Predict","Build Prediction Model","Predict","Which score value should I use for analysis.", "Quick Image","Saving Chemical Structures and Images","Saving Chemical Images","Insert Image", "How to Display a Binding Pocket Surface","How to Display the Residues Surrounding the Ligand Binding Pocket.", "icmPocketFinder","Small Molecule Docking","How can I find out which residues are surrounding a ligand binding pocket?", "How do I display only the residues that surround the ligand binding pocket?","How do I identify the binding pockets in my receptor?", "Displaying only the residues that surround the ligand binding pocket.","How do I show the sequence conservation around the ligand binding site?", "Pocket Display Options","How to Display a Binding Pocket Surface","How to Display a Binding Pocket Surface", "How to display and undisplay the ligand surface representation in the ICM 3D Ligand Editor.", "Image Preferences","Image Preferences","VLS Preferences","Protein-Protein Docking Batch", "Epitope Selection","Protein-Protein Make Receptor Maps","Display Grid Docking Results", "Protein-Protein Docking Procedure","Protein-Protein Ligand Setup","Protein-Protein Set Project", "Protein-Protein Receptor Setup","Using activeICM during a presentation","Advanced use of activeICM: Macros to direct visualisation changes", "When using ActiveICM is there a way to set a RELATIVE path to an icb file rath than ABSOLUTE?", "Predict Secondary Structure","Learn and Predict","Predict","Build Prediction Model", "Predict","What is considered a good druglikeness value?","Is there a way to build a classification model using the APF output?", "Predict","Predict","Preferences","Preferences","I would like to have a local copy of the PDB - any advice?", "I would like to have a local copy of the NCBI Blast database- any advice?","Insert a Dialog Box", "ActiveICM","Using activeICM during a presentation","Making Molecular Animations, Slides, and Documents", "I have made a H-Bond displayed in ICM-Browser-Pro which I would like someone to see in ICM-Browser - how do I do this?", "I have a small molecule which already has the 3D coordinates defined. How can I load the molecule and not optimize it so as to preserve the assigned 3D coordinates?", "Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "Preview and Export","Principal Component Analysis","A little theory on learning", "Print Plot","Save and Print Tree","Print Plot","Image Preferences","Optimize H, His, Asn, Gln and Pro", "When I setup the receptor I am asked to move a probe - what is this?","Problem with stereo?", "Troubleshooting","Defective graphics on a laptop or Windows computer with a low end graphics card.", "How to Save ICM Projects","Extract from ICB","Protein-Protein Set Project","Set Project Name", "Close Project","Save Project As","Labeling Atoms","Calculate Properties","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "How to Display Electrostatic Surfaces Around a Ligand.","Property Monitor","I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I have a small molecule displayed in 3D in a loaded PDB file. How can I extract this molecule into an ICM Chemical Table?", "What is considered a good druglikeness value?","I do not see the chemical property monitor in the molecular editor. Where is it?", "Property Monitor","Propogating a selection to all atoms in a residue.","Protect Shell Objects From Deletion", "Protect Shell Objects From Deletion","How to Read in a PDB File","How to Convert a Protein into an ICM Object", "How to Display Electrostatic Surfaces Around a Ligand.","Working with Sequences", "How can I merge two separate objects into one?","Protein Health","Protein Health", "Protein Health","Protein Interface by ODA","Protein-Protein Docking","Optimal Docking Area", "Protein-Protein Docking Procedure","Protein-Protein Set Project","Protein-Protein Receptor Setup", "Protein-Protein Ligand Setup","Protein-Protein Make Receptor Maps","Protein-Protein Docking Batch", "Display Grid Docking Results","Epitope Selection","ICM Convert","How do I change the tautomeric form of Histidine in a structure?", "Protein-Protein Docking","Property Monitor","Label Variables","How can I display the dihedral angle?", "Select by Purple 3D Box","How to Measure the Distance Between Two Atoms.","How to Convert a Chemical from the PDB", "How to Convert a Protein into an ICM Object","How to Make an Alignment using Drag and Drop", "How to Display Hydrogen Bonds Between a Ligand and Receptor.","How to Convert a Chemical from the PDB using the Graphical Display", "Converting a Chemical from the PDB using the ICM Workspace","How to Display the Residues Surrounding the Ligand Binding Pocket.", "How to Read in a PDB File","Making Basic Selections","Making Sequence Selections in the ICM Workspace", "How to Work With Sequences and Alignments","How to Load a FASTA Format File","How to Download a SwissProt sequence", "How to Make a New Sequence","How to Extract a Sequence from a PDB Structure.","How to Display Electrostatic Surfaces Around a Ligand.", "Build Prediction Model","Predict","Build Prediction Model","Predict","Does ICM support quad-buffer stereo?", "Write Image","General Preferences","Build Model","How do I perform a chemical search", "How do I make a new molcart database from a query search?","How do I perform a text query on a database in MolCart?", "Query Local Database","Querying PDB by Keyword or PDB Code","Querying PDB by Sequence Pattern", "Query Processing","Query Setup","How to Make a Picture","How to remove chain breaks (dotted lines)", "How to Move a Structure in the Graphical Display","How to: Protein Structure","How to load a PDB Structure", "How to Change Protein Representation","How to Make Selections","How to Change the Selection Level and Mode", "How to Make a Sequence Alignment","How to Check What is Selected","Display Distance Between Two Atoms - the quick way", "How to Color","Quit","Enumerate by Scaffold","Chemical View Options","Convert to Racemic", "Convert to Racemic","I am docking a racemic compound how can I sample both R andS states during docking?", "Making a Spherical Selection.","General Preferences","Display Rainbow, Box, Ruler", "Color Chemical Structure","Export Ramachandran Plot","Ramachandran Plot Interactive", "Export Ramachandran Plot","Change Speed, Range and Cycle Length of Animation","General Preferences", "Re-Dock and Minimize Ligand","Generating Chemical Fragments","Enumerate by Reaction", "Enumerate by Reaction","How to Read in a PDB File","Open","Reloading a Saved ICM Object when ICM is Running", "Recent Files","Searching the PDB","Loading Your PDB File","Load Sequence","Loading Chemical Structures", "Reading a Table","How to load a PDB Structure","PDB Search Results Table","How to Download a SwissProt sequence", "Working with Tables","Enumerate by Reaction","Mesh Clipping","Mesh Clipping","Recent Files", "Recent PDB Codes","Multiple Receptor Conformation Docking","Protein-Protein Receptor Setup", "Epitope Selection","I do not have ICM-VLS but I would like to calculate the binding energy of my docked complex - how can I do this?", "I want to dock to the receptor and include other molecules in the receptor such as a tightly bound water molecule - how can I do this?", "How can I run docking with a flexible receptor?","Multiple Receptor Conformation Ensemble Docking Example", "Receptor Considerations","How to display and undisplay the ligand surface representation in the ICM 3D Ligand Editor.", "Restore Recent Backup","Making Basic Selections","Making Sequence Selections in the ICM Workspace", "Redo","Redo","Undo and Redo","Regularization","Refine Side Chains","Refine Side Chains", "Epitope Selection","Least Squares Fitting","Learn","A little theory on learning", "Regularization","Regularization","Regularization","Find Related Chains","Learn and Predict", "Introduction","Reloading a Saved ICM Object when ICM is Running","Reloading a Saved ICM Object in Windows when ICM is not Running", "Reload a Docking Project","How do I reload a docking project?","Reload a Docking Project", "Reloading a Saved ICM Object in Windows when ICM is not Running","Reloading a Saved ICM Object when ICM is Running", "How to remove chain breaks (dotted lines)","If I have multiple graphical selections how can I remove one without losing the others?", "Can you suggest some ways to remove a selection completely?","I have the XYZ origin cross displayed - How can I undisplay this?", "Standardize Table","Standardize Table","Save Project As","How Do I renumber the residues in a PDB file", "Chemical Find and Replace","Find Best Replacement Group","Change Representations", "Save Viewpoint","Molecule Representations","Coloring and Changing Molecule Representations", "Font Preferences","What does as_graph mean?","How do I change the tautomeric form of Histidine in a structure?", "How can I select the closest residue from the center of mass of a selected residue?", "Labeling and Annotation","Label Residues","Residue Content","Label Residues","Propogating a selection to all atoms in a residue.", "Bioinfo Menu","Residue Content","How do I mutate a residue?","How do I mutate a terminal N or C residue?", "How to Display the Residues Surrounding the Ligand Binding Pocket.","How can I find out which residues are surrounding a ligand binding pocket?", "Move and Resize Mesh","Restore Recent Backup","Mesh Clipping","Mesh Clipping","Restore Recent Backup", "Working with PDB Search Results","Display Grid Docking Results","Docking Results - View Stack Conformations", "Review and adjust binding site","Enumerate by Scaffold","How to remove chain breaks (dotted lines)", "Ribbon Preferences","Display Tab","Structure Representation","Ribbon Representation", "Some structures are displayed as noodles (the \"worm\" representation). Why are they displayed improperly?", "How to remove the dotted lines in chain breaks.","Coloring and Changing Molecule Representations", "Molecule Representations","How to make a transparent ribbon?","Some structures are displayed as noodles (the \"worm\" representation). Why are they displayed improperly?", "Ribbon Preferences","Ribbon Preferences","Ribbon Representation","Ribbon Representation", "Ribbon Representation","Ribbon Representation","Ribbon Preferences","How to: Right Click Options", "How to: Right Click Options","Superposition","Rigid Substructure Superposition", "Rigid Superposition of Compounds in a Table onto a Template in The Graphical Display", "Right Click Options","Query Setup","Chemical View Options","Generate 3D Conformers", "Superposition","RMSD","RMSD","How can I calculate the RMSD between two protein structures?", "Can you give me some tips on which options to use for RMSD calcu","Superimpose Structures", "Animate View","Making Molecular Animations, Slides, and Documents","Molecular Animations and Transitions", "Make Animation","Rock","Change Speed, Range and Cycle Length of Animation","How can I calculate the RMSD between two protein structures?", "RMSD","How to Move a Structure in the Graphical Display","Animate View","Graphics and View Tools", "Move Buttons","Rotation","Custom Rotation","Rotate Chemical for Best-Fit","Making Molecular Animations, Slides, and Documents", "Molecular Animations and Transitions","Make Animation","Rotate","How to rotate a 2D chemical sketch so it fits nicely in its cell in a chemical table?", "Rotate Chemical for Best-Fit","Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "Easy Rotate","Change Speed, Range and Cycle Length of Animation","Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.", "How to use the Graphics window controls","Rotation","Working with Tables","Change Column and Row Width", "Copy Cut and Paste Row","Mark and Select Rows","Mark a Row","Mark a Row","How to show and hide columns and rows in a chemical spreadsheet.", "How to show and hide columns and rows in a chemical spreadsheet.","Display Rainbow, Box, Ruler", "How can I run the docking simulation from the UNIX command line?","How to remove salts, explicit hydrogens and standardize chemical groups.", "Superposition","Saving a Plot Image","Save and Print Tree","Saving an Animation", "ICM and AutoSave","Save and Append Chemical Structures","Saving a Plot Image","How to Save an ICM Object", "Save, Print and Delete","How to Save an ICM Project File","Add and Save Slide","Add and Save Slide", "Save a Table","Save and Print Tree","How to save a 2D sketch in mol format.","How to Make a Picture", "Write Image","How to save a 2D sketch in mol format.","How to Save an ICM Object", "Save with Password","Write Image","How to Save an ICM Project File","How to Save ICM Projects", "Save Project","Save Project As","Save Project Compatible with ICM 3_5","Table View Save", "Save Project","Save Project","Align/Color by 2D Scaffold","General Preferences", "Results - Scan Hits","Results - Scan Hits","How to Plot Histograms and Scatterplots of VLS Data", "To construct a scatterplot of your VLS data","VLS Results","Some compounds are missing from my HITLIST.", "What constitutes a good docking score?","Why is there always a small difference between the score calculated interactively by scanScoreExternal and that obtained by docking (VLS)?", "VLS Preferences","Docking Examples","Virtual Ligand Screening to Ricin Receptor", "Virtual Ligand Screening","Virtual Ligand Screening","VLS Getting Started","Movie Making", "Movie Making Options","Screen-grabbing Movie","Writing a Script in GUI.","Writing a Script in GUI.", "Insert Script","Insert a Dialog Box","How do I write a script to calculate solvent-accessible surface and tabulate the results to show area for each residue in a protein?", "FAQ-Script","How can I write a script in the Graphical User Interface?","I am having problems with my ICM script when running from the unix command line.", "How do I use the Dollar $ in ICM Scripts?","How to Import, Sketch, and Edit Chemicals", "How to make a local database.","Color Chemical Structure","Saving Chemical Structures and Images", "Saving from a chemical table.","Saving in the Molecular Editor","Saving in the ICM Workspace", "Saving Chemical Images","Molcart","How can I download the MolCart vendor compounds provided by MolSoft?", "I have a database in MolCart and I want to save it in SDF format - how can I do this?", "Virtual Ligand Screening to Cyclooxygenase","Browse Database","Pharmacophore","Molcart", "Molcart Search","How do I perform a text query on a database in MolCart?","Filter Search", "Search in Workspace","How to send a 3D pharmacophore search query.","Search in Workspace", "Assign Helices and Strands","How do I color a structure by secondary structure?", "Predict Secondary Structure","Bioinfo Menu","Ribbon Representation","Working with Tables", "Mark and Select Rows","How can I select the closest residue from the center of mass of a selected residue?", "Tree Selection","Selecting Amino Acids","Molecular Editor Selections","Select Duplicates", "Selecting Neighbors","Selecting Neighbors: Graphical","Selecting the Whole Object", "Display and Select Proteins for Superposition","Tree Selection","How to Make Selections", "How to Change the Selection Level and Mode","How to Check What is Selected","How to Make Selections", "How to Change the Selection Level and Mode","How to Check What is Selected","How to Make Selections", "How to Change the Selection Level and Mode","How to Check What is Selected","Select by Purple 3D Box", "How to Make Selections","How to Change the Selection Level and Mode","How to Check What is Selected", "How to Make Selections","How to Change the Selection Level and Mode","How to Check What is Selected", "Select All","Selecting Neighbors: Graphical","Plot Selection","Tree Selection","Tree View", "How do I specify a particular color for only the carbon atoms of a molecules?","If I have multiple graphical selections how can I remove one without losing the others?", "Can you suggest some ways to remove a selection completely?","What does as_graph mean?", "How can I select only the backbone atoms?","How to check on the display status of an object in the command line.", "I would like to delete all the residues in my protein except for the ones surrounding the ligand binding pocket.", "How do I display the distance between two atoms?","How can I select the closest residue from the center of mass of a selected residue?", "I want to dock to the receptor and include other molecules in the receptor such as a tightly bound water molecule - how can I do this?", "Making Graphical Selections","Making Basic Selections","Making Sequence Selections in the ICM Workspace", "Clear Selection","Neighbor Selection","Graphical Selections","Alignment and Table Selections", "Select All","Altering a Selection","Selecting Amino Acids","Selection","Graphical Selections", "Basic Selections","Altering a Selection","Clear Selection","Making Table Selections", "Selection","Filter Selection","Filtering a Selection.","Graphical Selections","Selecting Neighbors: Graphical", "Invert Selection","Making Table Selections","Graphical Selections","Selection Level", "Selection Mode","Neighbor Selection","Selection","Neighbor Selection","Selecting Neighbors", "Selecting Neighbors: Workspace","Selecting the Whole Object","Alignment and Table Selections", "Graphical Selections","Selection","Making Table Selections","Selection","Propogating a selection to all atoms in a residue.", "Making Table Selections","Selecting Neighbors","Neighbor Selection","Making a Spherical Selection.", "Display and Select Proteins for Superposition","Alignment and Table Selections", "Making Table Selections","Making Table Selections","Graphical Selections","Selection Tools", "Basic Selections","Altering a Selection","Filter Selection","Selecting the Whole Object", "Workspace Selections","Selecting Neighbors: Workspace","Invert Selection","Making Selections", "Link to Structure","Selecting Neighbors: Workspace","How to Download a SwissProt sequence", "How to Load a FASTA Format File","How to Make a New Sequence","How to Extract a Sequence from a PDB Structure.", "How to Make an Alignment using Drag and Drop","Bioinfo Menu","Multiple Sequence Alignment", "Working with Sequences","Load Sequence","Build Model","How do I show the sequence conservation around the ligand binding site?", "Working with PDB Structures","Working with Sequences and Alignments","Ligand Binding Pocket Analysis Examples", "Displaying the sequence conservation around the ligand binding site.","Bioinfo Menu", "Phylogenetic Trees","Sequence to Structure alignment","Set Sequence Type","Set Sequence Type", "How to Make a Sequence Alignment","Align Two Sequences","Drag and Drop","Set Sequence Type", "Set Sequence Type","Search and Align","Sequence to Structure alignment","How to Work With Sequences and Alignments", "Searching the PDB","Working with Sequences","I would like to have a local copy of the NCBI Blast database- any advice?", "Extract Unique Sequences","Extract Unique Sequences","Extract Unique Sequences", "Set Chemical Table 3D Browse Mode","How do I set a formal charge?","Edit Structure", "MMFF","Edit Structure","Making a disulfide bond.","How do I make a disulfide bond?", "Edit Structure","Edit Structure","Edit Structure","MMFF","Is there a way to build a classification model using the APF output?", "Protein-Protein Ligand Setup","When I setup the receptor I am asked to move a probe - what is this?", "Setup Ligand and Receptor","SGI ICM installation problem","Shading and Boxing an Alignment", "Occlusion Shading","Shadows","How do I color a structure by secondary structure?", "Shell Preferences","Labeling Residues","General Preferences","Light Tab","Graphics Preferences", "Hide and Show Columns","Hide and Show Columns","Chemical Table Side-by-Side View", "Chemical Table Side-by-Side View","Side-by-Side Stereo","Refine Side Chains","Fully Flexible Ligand and Receptor Docking", "Contour Electron Density Map","Convert Xray Density to Grid","Find Related Chains", "Compare Two Sets","How do I view a stack of solutions after a simulations?","FAQ-Simulations", "Editing structure using keyboard","How to Access the ICM Molecular Editor","Sketch Accents", "Sketch Accents","Display Tab","Structure Representation","Skin Representation","How can I change the color of a grob atom based surface according to the underlying atom coloring scheme?", "Coloring and Changing Molecule Representations","Molecule Representations","Mesh Clipping", "Mesh Clipping","Clipping Tools","Saving an Animation","Creating a Molecular Document", "Editing a Molecular Document","How do I set a blend transition effect between two slides?", "Slide Effects","Slide Navigation","Slide Navigation","Slide Effects","Slide Effects", "Slide Effects","Slide Effects","Making Molecular Animations, Slides, and Documents", "Making Molecular Slides","What is an iSee File?","How to Access the ICM Molecular Editor", "Loading Chemical Structures","Property Monitor","Calculate Properties","Convert Smiles to 2D", "Convert Structure to Smiles","How do I write a script to calculate solvent-accessible surface and tabulate the results to show area for each residue in a protein?", "Sorting the compounds in your HITLIST","Sort Table","Sorting the compounds in your HITLIST", "Data Clustering","Light Tab","What are the minimum specifications to run ICM on my computer?", "What are the minimum specifications to run ICM on my computer?","Change Speed, Range and Cycle Length of Animation", "sphere","sphere","How do I display only the residues that surround the ligand binding pocket?", "Displaying only the residues that surround the ligand binding pocket.","I would like to delete all the residues in my protein except for the ones surrounding the ligand binding pocket.", "How do I show the sequence conservation around the ligand binding site?","Displaying the sequence conservation around the ligand binding site.", "Making a Spherical Selection.","R-Group Decomposition","2D Depiction","How can I calculate the RMSD between two protein structures?", "Set Sequence Type","Viewing Your Docking Results","Display Grid Docking Results", "How do I view a stack of solutions after a simulations?","Standard ICM Tables","Standardize Table", "Standardize Table","Molcart Getting Started","Small Molecule Docking","I am having problems with my ICM script when running from the unix command line.", "Can you give me some tips on which options to use for RMSD calcu","Image Preferences", "Chemical View Options","Stereo Hardware Questions","Does ICM support quad-buffer stereo?", "Which stereo glasses?","Which stereo glasses?","Problem with stereo?","Hardware Stereo", "Side-by-Side Stereo","Stereo Hardware Questions","Convert to Racemic","How to generate stereoisomers.", "Generate Stereoismers","General Preferences","Molecule Representations","Still", "Interrupt Animation","Save Viewpoint","Saving an Animation","How can I store a view and return to it later?", "Save Viewpoint","How can I store a view and return to it later?","Protein Health", "I would like to delete all the residues in my protein except for the ones surrounding the ligand binding pocket.", "How to: Protein Structure","Biomolecule Generator","Learn and Predict","FAQ Structure", "Working with PDB Structures","Ligand Binding Pocket Analysis Examples","Structure Representation", "Convert Structure to Smiles","How to Display a Molecule","How to Display a Molecule", "Searching the PDB","Working with Chemistry Tools","Reading Chemical Structures", "General Preferences","Find and Replace","Molcart Search","Annotate By Substructure", "How do I perform a chemical search","How do I make a new molcart database from a query search?", "Annotate By Substructure","How do I write a script to calculate solvent-accessible surface and tabulate the results to show area for each residue in a protein?", "Making a disulfide bond.","Tools Menu - Superimpose","Superimpose","Superimpose", "Superimpose","I have multiple proteins overlayed and I would like to color the carbon atoms of each molecule uniquely - how can I do this?", "How do I superimpose two proteins?","How can I calculate the RMSD between two protein structures?", "Can you give me some tips on which options to use for RMSD calcu","Ligand Binding Pocket Analysis Examples", "Superimpose Structures","Proteins by 3D","Arrange as Grid","Multiple Proteins","Proteins by 3D", "Proteins by 3D","Arrange as Grid","Proteins by 3D","Flexible Substructure Superposition", "Proteins by 3D","Multiple Proteins","Rigid Superposition of Compounds in a Table onto a Template in The Graphical Display", "Rigid Substructure Superposition","Rigid Superposition of Compounds in a Table onto a Template in The Graphical Display", "Rigid Substructure Superposition","Flexible Substructure Superposition","Superposition", "How to Display Electrostatic Surfaces Around a Ligand.","General Preferences","Display Tab", "Structure Representation","Surface Representation","How can I change the color of a grob atom based surface according to the underlying atom coloring scheme?", "Surface Area","Surface Area","How to Convert a Protein into an ICM Object","Surfaces", "How to Display the Residues Surrounding the Ligand Binding Pocket.","How do I display only the residues that surround the ligand binding pocket?", "Displaying only the residues that surround the ligand binding pocket.","How to Download a SwissProt sequence", "Load Sequence","Crystallographic Neighbor","Biomolecule Generator","Crystallographic Analysis Tools", "PDB Preparation - Symmetry","Crystallographic Neighbor","System Preferences","Reading a Table", "Save a Table","PDB Search Tab","Working with Tables","Copy Cut and Paste Row","Change Column Format", "Mark and Select Rows","Plotting Table Data","Column Histogram","Plotting two columns", "Add a title to a plot","Change Axis Data","Change Mark Shape or Size","Change Mark Color", "Grid and Axis Display","Least Squares Fitting","Zoom, Translate and Center","Plot Selection", "Print Plot","Cluster","Display and Convert Molecule","Copy Molecule","Chemical View Options", "Zoom, Translate and Z-rotate a Chemical in a table.","Set Chemical Table 3D Browse Mode", "Rotate Chemical for Best-Fit","Color Chemical Structure","Pharmacophore","2D Depiction", "Generate 3D Conformers","Rigid Superposition of Compounds in a Table onto a Template in The Graphical Display", "How do I write a script to calculate solvent-accessible surface and tabulate the results to show area for each residue in a protein?", "How can I change the layout of a chemical table?","How can I convert a chemical in a chemical table into 3D?", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I have a small molecule displayed in 3D in a loaded PDB file. How can I extract this molecule into an ICM Chemical Table?", "Table Alignment","Clone a Table","Table Color","Change Column Format","Copy Cell", "Copy Selection to an ICM Table","Delete a Table","Editing a Table","Editing a Table", "Table Filtering and Appending","Table Search","Chemical Find and Replace","Table Font", "How to change font size in html-documents, alignments, terminal, table, graphics?", "Table View (Grid Layout)","Column Histogram","Inserting Columns","Table View (Grid Layout)", "Mark a Row","Mark a Row","Mouse and Cursor Actions on a Table","Basic Table Navigation", "New Table","Inserting Columns","Plotting Table Data","Print a Table","Rename a Table", "Table right click options","Saving a table","Saving a table","Table Search","Table Search", "Making Table Selections","Page Setup","Table Sorting","Split Chemical(s) into Fragments", "Table View (Grid Layout)","Table View (Grid Layout)","Table View Save","Zoom, Translate and Z-rotate a Chemical in a table.", "Mouse and Cursor Actions on a Table","Table Alignment","Table Filtering and Appending", "Clone a Table","Table Color","How to add columns into a chemical spreadsheet.","Inserting Columns", "Column Statistics","Hide and Show Columns","How to show and hide columns and rows in a chemical spreadsheet.", "How to compare two chemical spreadsheets.","How to copy, cut and paste columns and rows in a chemical spreadsheet.", "Mouse and Cursor Actions on a Table","Table right click options","Delete a Table", "Is there a way to determine the name of the current table displayed GUI?","Mouse and Cursor Actions on a Table", "How to edit data inside a chemical spreadsheet.","How to export your chemical spreadsheet into Excel.", "Export to Excel","Export to Excel","Export to Excel","How to filter columns in a chemical spreadsheet.", "Table Filtering and Appending","How to use find and replace in a chemical spreadsheet.", "Basic Table Navigation","Table Font","Is there a way to determine the name of the current table displayed GUI?", "Basic Table Navigation","Hide and Show Columns","How to insert hyperlinks to the PDB, PubMed, and Uniprot.", "Inserting Rows","Merge Two Sets","How to mark and label rows in a chemical spreadsheet.", "Page Setup","How to mark and label rows in a chemical spreadsheet.","How to merge two chemical spreadsheets.", "Merge Two Sets","Merge Two Sets","Mouse and Cursor Actions on a Table","Rename a Table", "Generate New Table","Table right click options","Page Setup","Page Setup","How to print a chemical spreadsheet.", "Basic Table Navigation","Print a Table","Reading a Table","Rename a Table","Table right click options", "Inserting Rows","Append Rows","How to save a chemical spreadsheet in sdf format.", "Saving a table","Basic Table Navigation","Save a Table","Page Setup","Basic Table Navigation", "How to save a chemical spreadsheet in sdf format.","Making Table Selections","Page Setup", "How to sort a column(s) in a chemical spreadsheet.","Table Sorting","Sort Table", "Standard ICM Tables","How to change the view of a chemical spreadsheet - form, table and grid.", "Chemical Table Side-by-Side View","Basic Table Navigation","Working with Tables", "Compare Two Sets","Generate Tautomers","How do I change the tautomeric form of Histidine in a structure?", "How to generate tautomers.","Generate Tautomers","Local Flexibility","Build Model", "Superposition","How can I guide my docking to a known conformation of a smilar ligand?", "Chemical View Options","How to change font size in html-documents, alignments, terminal, table, graphics?", "Font Preferences","Chemical View Options","Molcart Search","Making Molecular Documents", "Creating a Molecular Document","Editing a Molecular Document","Document Navigation", "How do I perform a text query on a database in MolCart?","Annotation","Search a Database by Text", "Meshes Tab","Generate 3D Conformers","Superposition","What does thoroughness mean?", "Display and Convert Molecule","I have a small molecule which already has the 3D coordinates defined. How can I load the molecule and not optimize it so as to preserve the assigned 3D coordinates?", "General Preferences","How to Move Windows","How to Move Windows","How long does it take to dock one ligand using ICM-VLS?", "Tools Menu - 3D Predict","Tools Menu - Analysis","Append Rows","Tools Menu - Extras", "Plot Function","icmPocketFinder","Protein Interface by ODA","Tools Menu - Superimpose", "Tools Menu - Table","Build Prediction Model","Cluster Set","Merge Two Sets","Predict", "Torsion Angles","How can I change the torsion angle?","Move Buttons","Torsion Angles", "How to Incorporate Transition Effects Between Slides","How do I set a blend transition effect between two slides?", "Making Molecular Animations, Slides, and Documents","What is an iSee File?","How to Move a Structure in the Graphical Display", "Graphics and View Tools","Move Buttons","Zoom, Translate and Z-rotate a Chemical in a table.", "How to use the Graphics window controls","Six Frame Translation","Translation","Translation", "Zoom, Translate and Center","Color and Mesh Display","How to make a transparent ribbon?", "Tree Selection","Save and Print Tree","Tree View","Phylogenetic Trees","Phylogenetic Trees", "Phylogenetic Trees","How to reorder branches and change the distance of trees.", "How to edit the tree - labels, spacing and coloring.","How to reorder branches and change the distance of trees.", "ICM graphics crashes.","Defective graphics on a laptop or Windows computer with a low end graphics card.", "Troubleshooting","How to truncate a mesh object?","ICM crashes, or hangs if you are trying to start the Chemical Editor, or a Query window", "Save a Table","PDB Preparation - Occupancy and B-Factors","PDB Preparation - Symmetry", "Ligand Binding Pocket Analysis Examples","Displaying hydrogen bonds between a ligand and receptor.", "Displaying only the residues that surround the ligand binding pocket.","How to Incorporate Transition Effects Between Slides", "How to Make a Molecular Document","Multiple Receptor Conformation Ensemble Docking Example", "Displaying the sequence conservation around the ligand binding site.","Working with the Graphical Display", "Making Graphical Selections","Coloring and Changing Molecule Representations","Molecule and Background Coloring", "Molecule Representations","Labeling and Annotation","Working with PDB Structures", "PDB Searching","Converting a PDB File into an ICM Object","Pairwise Alignments", "Sequence Drag and Drop and the Alignment Editor","Multiple Sequence Alignments", "Boxing Shading and Annotating an Alignment","Homology Modeling and Structure Analysis Tools", "Homology Modeling","Linked Alignments and Structures","Making an amino acid mutation", "Protein Health","Biomolecule Generator","Superimpose Structures","Draw Chemical", "Chemical Similarity Searching","Advanced Chemical Similarity Searching","Docking Examples", "Re-Dock Biotin to the Streptavidin Receptor","Re-Dock an Inhibitor to Ricin Crystal Structure", "Virtual Ligand Screening to Ricin Receptor","Virtual Ligand Screening to Cyclooxygenase", "How to Build Fully-Interactive 3D Molecular Documents (iSee File)","Getting Started", "2D Pharmacophore Searching","3D Pharmacophore Searching","Chemical Searching","Edit Chemical", "Tutorials","Tween","Display and Convert Molecule","I have a small molecule which already has the 3D coordinates defined. How can I load the molecule and not optimize it so as to preserve the assigned 3D coordinates?", "Mesh Clipping","Mesh Clipping","How to use the ICM Workspace Panel","Display and Undisplay Hydrogens", "I have the XYZ origin cross displayed - How can I undisplay this?","How to check on the display status of an object in the command line.", "(Un)display Origin","Preferences","Undo","Undo","Undo and Redo","Undo and Redo", "How to Download a SwissProt sequence","Chemical View Options","Select Duplicates", "Biomolecule Generator","What are the units of the energy values displayed after docking?", "I am having problems with my ICM script when running from the unix command line.", "Introduction","Using activeICM during a presentation","Introduction","Molcart Administration", "Annotation","A dictionary of chemical groups.","Undisplay All","Display Clash","Font Preferences", "What does as_graph mean?","Labeling and Annotation","Generate 3D Conformers","Generate 3D Conformers", "Movie Making","Movie Making","Movie Making Options","Movie Making Options","Save Viewpoint", "Chemical View Options","How can I store a view and return to it later?","How do I view a stack of solutions after a simulations?", "Center","Color Background","Viewing Your Docking Results","Macro Shape","View Menu", "Mesh Clipping","Selection Level","Selection Mode","View Menu","View Tools","Tree View", "Undisplay All","Stack","Virtual Ligand Screening","Virtual Ligand Screening","VLS Getting Started", "Docking Examples","Virtual Ligand Screening to Ricin Receptor","Biomolecule Generator", "Flexible Receptor Docking and Multiple Receptor Conformations","Virtual Ligand Screening", "Run VLS in the Graphical User Interface","Some compounds are missing from my HITLIST.", "What constitutes a good docking score?","Virtual Ligand Screening to Cyclooxygenase", "VLS Getting Started","To construct a histogram of your VLS data","How to Plot Histograms and Scatterplots of VLS Data", "Virtual Ligand Screening","VLS Preferences","VLS Results","Run VLS in the Graphical User Interface", "To construct a scatterplot of your VLS data","VLS Results","Property Monitor","Virtual Screening Examples", "Meshes Tab","How do I display weak hydrogen bonds?","Export as ActiceICM Html","Calculate Properties", "I have a chemical table displayed - how can I add columns of chemical properties associated with each chemical in my table?", "I do not see the chemical property monitor in the molecular editor. Where is it?", "Cluster","Ligand Considerations","Change Column and Row Width","How to Move Windows", "Edit Slide Description","How to Arrange Windows","Molcart Installation","General Preferences", "Display Tab","Structure Representation","Wire Representation","How do I specify a particular color for only the carbon atoms of a molecules?", "How can I display a structure in many different representations simultaneously?", "Coloring and Changing Molecule Representations","Molecule Representations","Bonds Preferences", "Working with PDB Search Results","Working with Sequences and Alignments","Working with the Molecular Editor", "How to use the ICM Workspace Panel","Converting a Chemical from the PDB using the ICM Workspace", "Converting a Chemical from the PDB using the ICM Workspace","Making Sequence Selections in the ICM Workspace", "How to use the ICM Workspace Panel","Workspace Selections","Workspace Navigation", "How to Make a Picture","Saving a Plot Image","I have a database in MolCart and I want to save it in SDF format - how can I do this?", "How do I make a movie of my montecarlo simulation and write all output.","Write Image", "Write Image","How to Save an ICM Object","Write Image","How to Save an ICM Project File", "Save Project","Saving a table","How to write a pdb file?","Tools Menu - Xray","Label Variables", "How can I display the dihedral angle?","Stick and Ball (Xstick) Representation", "How can I display a structure in many different representations simultaneously?", "Molecule Representations","I have the XYZ origin cross displayed - How can I undisplay this?", "How to Move a Structure in the Graphical Display","How to use the Graphics window controls", "Graphics and View Tools","Move Buttons","Zoom","Zoom","Zoom, Translate and Center", "Zoom, Translate and Z-rotate a Chemical in a table."); var paths=new Array("labels-tab.html#custom-label","chemical-spreadsheets.html#convert-chemical","chemical-spreadsheets.html#chem-view", 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