[Chimera-users] View Dock plugin

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 22 17:22:56 PDT 2013


Dear James,
(1) The sidechains near the ligand are not necessarily shown, so I would not assume that they are all shown.

However, you can certainly hide any sidechains that are shown (which would also hide H-bonds to/from those sidechains).  For example, the following command would hide all atoms/bonds of model #0:

~display #0

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/display.html>
(you can use the Favorites menu to show the Command Line if it isn't already shown)  If you aren't sure of the model numbers of receptor and ligands, one way to tell is to look in the Model Panel (also under Favorites menu).

The ribbon would still be displayed.  If there are hbonds between parts of the ribbon, you can delete all hbonds with the following, but then you would need to recalculate hbonds if you want to show them later.

~hbond

If the receptor is #0 and the ligand you are viewing is #1.8, you could show only (i.e. hiding other atoms) the receptor residues within 4.5 angstroms of that ligand with the command:

show #0 & #1.8 z<4.5

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/show.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combinations>

(2) Before saving a PDB file, you can combine specified models using the "copy/combine" function in the Model Panel, or the command "combine," for example to make new model 5 from 0 and 1.8:

combine #0#1.8 modelId #5

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
Then you could save the new model #5 to a file.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 21, 2013, at 12:38 AM, James Starlight wrote:

> Dear Chimera users!
> I have a question about the View Dock plugin. 
> From some servers usually I've obtained pdb file of the target protein as well as separate file consisted of all predicted posses which I can visualize in Chimera. 
> 
> So I wounder to know
> 
> 1- How I could hide hydrogen bonds as well as protein's side chains of the residues which are in contact with the ligands ( on the default both of that two options are turned ON)
> 
> 2- How I could properly save some poses as the separate pdb models ? E.g when I chose to same target.pdb with the #1_pose from the chimera saving menu I obtain protein and ligand with the surrounded residues as two models in one pdb file ( so I must manually merge it in one model and delete residues from the second model). Does it possible to obtain protein-ligand complex as one model as the output?
> 
> Thanks for help,
> James




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