Sep 4 2023
[ Font Size | Background color | Transparent ribbon | Color carbons | Color carbons multiple objects | Faq remove select | Faq deselect | as_graph | Orange Selection | Faq origin | Faq clipping plane | Faq interactions | Faq backbone | icmPocketFinder | Truncating Mesh | Color surface | Faq atom display | Dihedral Angle | Movie | Color faq | Plane faq | Store current view faq | Ribbon faq | Local PDB | Local PDB | ODA | Faqmaps | Faqcontour | H-Bond Cutoff | iSee file | Blend Transition | Object Status | Faq autosave | Chain Breaks | Beep | Residue Number Selection | Smooth Surface | Color Scale | Row Height ]
Questions and answers relating to displaying molecules in the graphical user interface.
First, click on this window of interest. Then just press Ctrl-+ (Ctrl-plus) to increase the font size and Ctrl-- (Ctrl-minus) to decrease the font size.
Here is a more complete list of methods to change the font size:
The sizes will also be preserved between sessions.
To change the background color with one mouse click, go to the Display toolbar and right click on the color you like. Warning: the left click on the same palette will color all the object, but will preserve the background color. The ICM command for changing the background is
color background red # or any other color
To make a transparent ribbon follow these steps:
One way to do this is to use the Remove selection button shown below and then drag over the region you would like to remove using the right-click mouse button.
Some other ways include:
By default anything that is selected (object, molecule, residue, atom) is returned to a variable called as_graph. If you type as_graph in the terminal window you will see all the atoms, residues, molecules or objects contained in as_graph. You can also rename as_graph to a different variable name in order to save it for other functions. For example:
my_binding_pocket=as_graph ds wire my_binding_pocket
To list the residues surrounding the pocket type:
The orange selection provides a convenient way to have two selections (green and orange). Click here to learn how to transfer a green selection to an orange selection.
To undisplay the origin shown below:
It looks like the clipping tools have been used to clip away the front and back planes. Use the "unclip" button ( See the section entitled Clipping Tools).
To do this first you need to display the distance.
Sometimes you have a mesh object (a.k.a. grob in ICM language) and you want to crop it. This can be achieved with the "make mesh from display"-tool (the "Mesh" toolbar) that creates a mesh object from the all visible objects in the Graphics window. The trick is to use the window border as a trimming device by moving the unwanted parts of the mesh outside the Display window. Follow these steps:
To do this:
To label the dihedral angle the molecule needs to be converted into an ICM object.
The easiest way is to interpolate between front and back clipping plane
v1=View() # define the 1st view # v2=View() # cut through clipping plane for i=1,100 set view View(v1,v2,i*0.01) # interpolation write image String(i) png endfor
You may wish to color your structure accordingly:
Helix: Red Beta Sheet: Green Loops: White
To do this you should use the filter graphical selection button and then select either H, E or _ for helix, sheet or loop. Then click on the color panel in the display tab.
Use the slide button and make a series of slides.
To store multiple views of an object and quickly change between each one use the "eye" button shown below.
For more information see the section entitled Store Current View
There are several possible reasons:
Accessing PDB files locally
The simplest way to access pdb files locally, is to download the compressed pdb files in the old pdb format (not the mmcif files!) from the PDB ftp site and reset the values in File/Preferences/Directories .
By default ICM will set the s_pdbDir and pdbDirStyle variables to download each file from the PDB web site. In this case to update the PDB table of entry headers and the blast files with PDB sequences, select Edit/PDBSearch and click on the "Update PDB Table" button for the headers and the "Update PDB Sequences" button for the sequences.
Accessing the NCBI sequence databases locally
To enable ICM sequence search simply dowload NCBI blast database files to the local s_blastdbDir directory (see File/Preferences/Directories ). Download only three file types for the databases of interest: *.pin, *.phr, *.psq , e.g. nr.pin,nr.phr,nr.psq to your s_blastdbDirectory ( File/Preferences/Directories ) or anywhere else. You can download Blast formatted databases from here ftp://ftp.ncbi.nih.gov/blast/db/ eg. pdbaa - PDB sequence database.
ICM command find database and the Bioinfo/Find_and_Align macro can then use the blast files for both fast searches and ZEGA searches.
The Optimal Docking Area (ODA) tool is used to predict protein-protein interaction sites.
You can load CCP4 maps into ICM
Load the electron density map into ICM and then follow the instructions in the section entitled Contour Electron Density Map.
GRAPHICS.hbondMinStrength parameter determines the hbond strength threshold for hbond display. The strength value is between 0. and 2. By changing 1. to 0.2 you will see weaker hydrogen bonds.
A common question is - what is an iSee file? An iSee file is a term coined by scientists at the Structural Genomics Consortium at Oxford University for ICM molecular documents saved in .icb format.
>From the SGC website:
"Different from PDF files and paper manuscripts, iSee files allow total interactivity with the scene/ image by the user. Also, real-time rendered movies enable smooth transition of a viewpoint to another, helping to convey the sense of depth and inter-relationship of different structural features in space. iSee files also permit non- linear navigation through the expert annotation, thus not restraining the user to the sequential explanation of traditional molecular movies."
In ICM version 3.5-1l a new blending transition effect between slides is available. To see this in action download the latest version of ICM or the free ICM-Browser and view this icb file:
To generate this transition effect:
You can check if molecule is displayed by using 'DD' selector.
Mol(a_1xbb.a//DD) == a_1xbb.a # returns 'yes' if at least one atom in the molecule is displayed Res(a_1xbb.a//DD) == Res(a_1xbb.a) # returns 'yes' if at least one atom in each residue is displayed Atom(a_1xbb.a//DD) == Atom(a_1xbb.a) # returns 'yes' if every single atom is displayed
There are two preferences controlling 'autosave/restore behaviour'
GUI.autoSave # toggles autosave on/off GUI.autoSaveInterval # autosave interval in min.
If ICM crashes it renames the last autosaved file to 'icmcrash' prefix. On startup ICM checkes if s_tempDir directory contains at least one file with prefix = 'icmcrash' and offers to restore session from it. 'icmautoXXXX' and 'icmcrashXXXX' are normal icm files and can be copied/renamed and read directly with 'read binary' or through GUI.
ICM deletes 'icmautoXXXX' file before normal exit. Note that in certain cases these files will be kept. E.g: if you press "Ctrl+C" on linux will not receive crash signal -> 'icmauto' will not be renamed to the 'icmcrash' and will be kept.
In version 3.6-1a and above you can use the options in the display tab. Click and hold on the ribbon button. You can then select Display Chain Breaks/ None.
To turn off the beep noise when an error is made in the command line type:
l_beep = no write system preferences # if you want to store this permanently
You can also remove it in the system preferences tab in File/Preferences
This is a common question primarily because this option is hidden! It is hidden for a reason because the residue numbers you enter can only relate to one molecule in a particular object. Therefore to find this option you need to right click on the molecule name in the ICM Workspace and choose Select/by Res.Number. You can then enter the residue numbers e.g 3,7:12,30 and the selection will be made. If you want to make a selection on multiple molecules you can change the selection mode to add ( http://www.molsoft.com/gui/make-selection.html#change-selection ) and repeat the steps described above.
To display the scale:
See the documentation here.
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