[ Peptide | Compound | DNA/RNA | Sequences | Objects | Script | HTML | New Table | Arrow | box | sphere | 3D Label ]

ICM can read as well as create several different entities. This dialog box helps you to create new entities from scratch:

All the processes in this section can be found under File/New, in the New molecule/sequence/grob window

3.1.1 Constructing a New Peptide

Creates a peptide as a new ICM Object, named after the string entered in the 'Object name' field. The residue composition of the new peptide is the string entered in the 'One Letter Code' field. The chemical property of the peptide ends will be created according to the type of terminus choosen from the 'N-terminus' and 'C-terminus' drop-down list.

The peptide can be displayed immediately after creation (check the 'Display molecule' option). All other objects can be deleted before the creation of the new object (check the 'Delete other objects' option). The new peptide can be folded as an alfa-helix (phi= -62 deg.; psi= -41 deg.), instead of a linear stretch of residues (phi,psi = 180 deg.) (check the 'Assign A-helix' option).

Please note that the created peptide will not be in its most favorable energetic conformation.

To construct a new peptide:

• Select File/New and the New molecule/sequence/grob window will appear.
• Type the peptide sequence into the One letter code data entry box. Remember to delete the previous entry if it is in the box.

NOTE: If the peptide you wish to make has been made previously then it will be in the drop down menu in the One letter code box.

• Select the appropriate N-terminal and C-terminal from the drop down menu.
• Check the boxes Display Molecule Delete Other Objects Assign A-Helix (Alpha Helix) according to your particular preference.
• Click the OK button.

3.1.2 Constructing a New Compound

Creates a compound/ small chemical molecule, based on the SMILES - Simplified Molecular Input Line Entry Specification - string supplied. The name of the compound can be specified on the 'Object name' field. For further information on SMILES syntax http://www.daylight.com/dayhtml/smiles.

The new compound can be displayed immediately after creation (check the 'Display molecule' option). All other objects can be deleted before the creation of the new object (check the 'Delete other objects' option).

Please note that the created compound will not be in its most favorable energetic conformation.

To construct a new compound:

• Select File/New and the New molecule/sequence/grob window will appear.
• Click the Compound tab at the top of the window.

OPTION 1:

• Type in the Smiles String in the Smiles String data entry box. Remember to delete the previous string. If a string has been entered previously it will be available by clicking on the drop-down button.
• Check the boxes Display Molecule Delete Other Objects according to your preference.
• Click the OK button.

OPTION 2:

• Click the Launch Molecule Editor button.

Please refer to the Launch Molecule Editor section of this manual for instructions.

3.1.3 Constructing New DNA or RNA

Creates a nucleic acid chain object - either DNA or RNA, according to the selection and the nucleotide sequence. The sequence should be supplied in one-letter code (ATCG) format, starting from 5' end. The name of the DNA/ RNA object can be specified on the 'Object name' field.

If the 'DNA duplex' option is selected, the complementary strand will be created automatically as a separate molecule in the same object.

The new DNA/ RNA can be displayed immediately after creation (check the 'Display molecule' option). All other objects can be deleted before the creation of the new object (check the 'Delete other objects' option).

Please note that the DNA/ RNA will be created as adopting the canonical B-DNA conformation.

To construct new strand of DNA or RNA:

• Select File/New and the New molecule/sequence/grob window will appear.
• Click the Nucleotide tab at the top of the window.
• Check the appropriate box for the nucleotide you are constructing, either DNA RNA or DNA Duplex
• Enter the nucleotide sequence into the One Letter Code data entry box. Remember to delete the previous nucleotide sequence. If a sequence has been entered previously it will be available by clicking on the drop-down button.
• Check the boxes Display Molecule or Delete Other Objects according to your preference.
• Click the OK button.

3.1.4 Constructing New Protein and Nucleic Acid Sequences

Creates a new Sequence using the information supplied by the user in FASTA format. The sequence type can be defined as protein or nucleic acid by the user, or automatically detected by ICM. Simply choose one of the options on the dialog box. The sequence name can be specified in the 'Sequence name'.

To construct a new protein and nucleic acid sequence:

• Select File/New and the New molecule/sequence/grob window will appear.
• Click the Sequence tab at the top of the window.
• Copy and paste a Fasta-format sequence into the Sequence data entry box.
• ICM will automatically determine what kind of sequence you have constructed but if you wish to specify then you can check either the protein or nucleic acid box.
• Click the OK button.

3.1.5 New Graphical Objects

To construct a new graphical object, such as a arrow, box, sphere, or text:

• Select File/New and the New molecule/sequence/grob window will be displayed.
• Click the Arrow, Box, Sphere, or Text tab at the top of the window, according to your desired object.
• Adjust the color and size of your graphical object.
• Click the OK button.

3.1.6 Writing a Script in GUI.

Creates a clickable link on the workspace that launches scripts written using ICM language. The link is named after the 'Script Name'.

There are two ways of defining the script to be associated with the link. The first is to input the ICM script directly into the 'IcmCode' field. Alternatively, a file containing an ICM macro can also be associated with the link.

To write a script in the graphical user interface:

• Select File/New and the New molecule/sequence/grob window will be displayed.
• Click the Script tab at the top of the window.
• Write your ICM script in the text box provided (see below) and click OK.

To run or edit your script:

• Right click on the script name in the ICM workspace.

NOTE: For more details regarding the ICM scripting language please see the separate ICM language manual.

3.1.7 HTML

• File/New HTML tab privides a window to enter HTML code. This window is a good starting point for generating new molecular documents.

3.1.8 New Table

To generate a new empty table:

• File/New and select the Table tab and a window as shown below will be displayed.
• Enter the number of rows and columns you wish to include in your table and whether you wish to add a column with chemical data.

3.1.9 arrow

Creates a 3D arrow as a new graphical object ('grob' or 'mesh'). This arrow can be generated both as a solid object or as a simpler line representation. The name of the object can be defined in the 'Arrow Name' field.

The start (StartXYZ) and end (End XYZ) points of the arrow are defined in cartesian coordinates (X, Y, Z). The quality of the arrow can be adjusted (the higher the value, the smoother the arrow will be). Color can be assigned by simply clicking on the desired one or using rgb scale (eg. for red: rgb={1. 0. 0.}).

The Arrow Radius is defined in Angstroms. The size of the head, shown as a solid cone is defined as a fraction of the whole lenght of the arrow. Thus 0.1 means that the height of the head will take 10% of the total size of the arrow, while 1.0 means that the head will take the whole arrow (resulting in a shaftless arrow). The width of the head refers to the diameter of the head cone and it is defined as a multiplier of the Arrow Radius.

Tip: the arrow can be moved independently using 'connect'

3.1.10 box

Creates a 3D box as a new graphical object ('grob' or 'mesh'). This box can be generated both as a solid object or as a simpler wire representation. The name of the box can be defined in the 'BoxName' field.

Dimensions of the box (X, Y, Z) are given in Angstroms and the angles connecting the sides are given in degrees. Color can be assigned by simply clicking on the desired one or using rgb scale (eg. for red: rgb={1. 0. 0.}).

Tip: the box can be moved independently using 'connect'

3.1.11 sphere

Creates a 3D sphere as a new graphical object ('grob' or 'mesh'). This sphere can be generated both as a solid object or as a simpler wire representation. The name of the sphere can be defined in the 'BoxName' field.

Dimensions of the sphere (X, Y, Z) are given in Angstroms and the angles connecting the sides are given in degrees. Color can be assigned by simply clicking on the desired one or using rgb scale (eg. for red: rgb={1. 0. 0.}).

Tip: the arrow can be moved independently using 'connect'

3.1.12 3D Label

Creates a text label that can be placed and repositioned in the 3D space of the GL window. The text to be displayed can be entered in the 'label text' field and the name for the label can be entered in the 'Label Name' field. Color can be assigned by simply clicking on the desired one or using rgb scale (eg. for red: rgb={1. 0. 0.}).

Once the 'OK' is hit, the label is displayed and automatically connected (see connecting [ADD LINK]). At this stage, the label can be moved and repositioned. Disconnect the label (hit the 'esc' key on your keyboard) to resume working.