[ Related Chains | RMSD | Contact Areas | Closed Cavities | Surface Area | Distance | Planar Angle | Dihedral Angle | Ramachandran Plot | Ramachandran Export ]

Note: Click Next (top right hand corner) to navigate through this chapter. Headings are listed on the left hand side (web version) or by clicking the Contents button on the left-hand-side of the help window in the graphical user interface.

3.7.1 Find Related Chains

This option allows you to search the currently loaded PDB files or ICM objects and identify chains which are similar and/or related.

You can do this by:

• Select the objects or pdb files you want to compare.
• Tools/Analysis/Find Related Chains
• Click OK to confirm the selection you made
• A table as shown below will be displayed.

name1 = Name of query structure molecule name2 = Name of hit len1 = length of query len2 = length of hit seqid = Sequence identity percentage consensus = Consensus sequence

3.7.2 RMSD

NOTE: This option is for protein structures only not for chemical compounds. You can use the command line options RMSD and SRmsd for chemicals.

To calculate RMSD between two structure:

• Read into ICM the two structures (File/Open or PDB Search or Read in Chemical)
• Select the two structures you wish to superimpose. You can do this by double clicking on the name of the structure in the ICM Workspace (a selection is highlighted blue in the ICM Workspace and green crosses in the graphical display} or you can use the right-click button and drag it over the whole structure in the graphical display. Use the CTRL key to select more than one object in the ICM Workspace or use the add selection button if selecting more than one object in the graphical display.
• Tools/Analysis/RMSD and a window as shown below will be displayed.

• Select whether you wish the atoms to be superimiposed onto one another or kept in place. The kept in place option would be ideal for compating docked structures.
• Choose whether you wish to make the superposition by alignment or exactly matching the atom names.
• Select which atom types you wish to superimpose.

The RMSD value will be displayed in the terminal window.

3.7.3 Contact Areas

• Read in a protein structure (File/Open or PDB Search)
• Select the region you wish to analyse.
• Tools/Analyze/Contact Areas
• The xstick display in the region will be scaled according to the atom/residue contact area. For example, residues making large contacts with a ligand will be displayed in thicker xstick representation than those making small contacts.
• A table as shown below will be displayed. Residues making key contacts will be displayed in xstick (radius represents contribution size). Carbon atoms are colored light green, nitrogen atoms are colored light blue and oxygen atoms are colored light red. The table lists the contact area, exposed area and the percentage of contact area compared to exposed.

NOTE: You can slso right click on the molecule in the ICM Workspace and select "Analyze Residue Contacts"

3.7.4 Closed Cavities

This tool will identify cavities within a molecule which are completely closed,. If you are looking for buried and open pockets then use icmPocketFinder.

• Read in a protein structure (File/Open or PDB Search)
• Tools/Analysis/Closed Cavities
• Use the drop down arrow to locate the receptor you are interested in.
• Enter the minimum volume of the cavities you wish to identify.
• Click OK
• The closed cavities will be displayed in the meshes section of the ICM Workspace and a table of the cavities will be displayed. Double click on a row in the table to jump to a particular closed cavity and select the residues surrounding it.

3.7.5 Surface Area

This option calculates solvent accessible area of each selection in multiple objects and stores it in a table. If a molecule is specified in a multi-molecular object, the surface area of an isolated molecule is calculated and other molecules are ignored. The area is reported in square Anstroms and the probe radius is assumed to be the value set in the variable waterRadius.

Output: the macro creates table AREA . The empty comment field is added for user's future use. If the table exists, new rows are appended.

To calculate a surface area:

• Read in a protein structure (File/Open or PDB Search)
• Select the region you wish to analyse.
• Tools/Analysis/Surface Area
• A table will be displayed listing the residues in the selection along with the corresponding total surface area.

3.7.6 Distance

There are two approaches to calculating and displaying distances between atoms. You can either use the options in the Labels tab or use Tools/Analysis/Distance

To display all to all distances:

• Select the atoms between which you would like to find the distance. (See selection toolbar)
• Tools/Analysis/Distance
• Select all to all

To display intermolecular distances

• Select the atoms between which you would like to find the distance. (See selection toolbar)
• Tools/Analysis/Distance
• Select intermolecular

To display the distances between the same atoms in two objects.

• Select the atoms between which you would like to find the distance. (See selection toolbar)
• Tools/Analysis/Distance
• Select same atoms in two objects

You can also use the buttons in the label tab to display the distance between two atoms:

• Click on the labels tab (previously called advanced tab).
• Select the atoms between which you would like to find the distance. (See selection toolbar)
• Click on the 'Show Distances Between Two Atoms' Button
• The distance will be displayed in angstroms, in green.

To find the distance from one atom to many:

• Click on the labels tab (previously called advanced tab).
• Select the atom from which you wish to measure the distance from (See selection toolbar)
• Click on the 'Show Distances From One Atom To Many' button.
• The distances will be displayed in green.

The maximal and minimal distances can be selected by entering values in the boxes shown here (below) in the labels tab (previously called Advanced tab).

NOTE: Distances can be displayed and undisplayed in the 3D labesl section of the ICM Worskapce (left hand side of graphical user interface). You can change the color of a distance label by right clicking on it in the ICM Workspace. You can alse export the distance to a table.

3.7.7 Planar Angle

If you wish to find the planar angle between three atoms:

• Select Tools/Analysis/PlanarAngle

• Right click on the each of the three atoms which you wish to use, and select their name. The spaces next to First atom, Second atom, and Third atom should now contain the name of your atoms.

• Click Apply to display the angle measure in the terminal window.

3.7.8 Dihedral Angle

In order to find the angle dihedral angle between two sets of atoms:

• Select Tools/Analysis/Dihedral Angles.

• Right click on each of the four atoms which you wish to use, and select the name of the atoms. The spaces next to Atom 1, Atom 2, Atom 3, and Atom 4 should now contain the names of your atoms.

• To find the correct angle, select your atoms according to the following diagram:

• Click Apply to display your dihedral angle measure in the terminal window.

3.7.9 Ramachandran Plot Interactive

To make an interactive ramachandran plot:

• Read in a protein structure (File/Open or PDB Search)
• Select the structure you wish to build the plot for. You can do this by double clicking on the name of the structure in the ICM Workspace (a selection is highlighted blue in the ICM Workspace and green crosses in the graphical display) or you can use the right-click button and drag it over the whole structure in the graphical display.
• Tools/Analysis/Ramachandran Plot Interactive
• The interactive ramachandran plot will be displayed in table called RAMA.
• You can view the Omega, Phi/Psi (Gly) or Phi/Psi angles by clicking on the tabs at the top of the plot. Each point is linked to the data in the table RAMA and also to the graphical display. Soby clickin on a point in the plot will highlight the corresponding angles in the table and also center on this region in the 3D display.

3.7.10 Export Ramachandran Plot

• Read in a protein structure (File/Open or PDB Search)
• Select the structure you wish to build the plot for. You can do this by double clicking on the name of the structure in the ICM Workspace (a selection is highlighted blue in the ICM Workspace and green crosses in the graphical display) or you can use the right-click button anddrag it over the whole structure in the graphical display.
• Tools/Analysis/Ramachandran Plot Export

A postscript viewer needs to be downloaded onto your machine in order to view the plot. This can be downloaded from http://www.cs.wisc.edu/~ghost/. Once this software is downloaded you need to tell ICM where it is located by typing the pathname into File/Preferences.

NOTE: You can always export the plot as an image directly in ICM without exporting. You can do this by right clicking on the plot and select save as image. Another approach could be to export the RAMA table to Excel and use the plotting tools there. You can do this by right clicking on the table name tab and selecting "Export to Excel" or save as ".csv".