[Chimera-users] ViewDock

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 23 14:25:51 PDT 2015

Dear Leila,
Try Chimera commands something like this:

alias ^savecplx ~modeldisp #1;modeldisp #1.$1; combine #0#1.$1 model #2;write relative #0 #2 ~/Desktop/receptor-lig$1.pdb;close 2
perframe savecplx range 1,252

That example assumes the receptor is opened as model 0 and the ligands as model 1 (1.1… 1.252 in your case).  The alias command ending with “close 2” must be all one line (don’t break it into multiple lines even if your mail display makes it look that way).  You could name the alias and the output files differently, as you like. The combining is required because the “write” command only saves one model at a time.  The "File… Save PDB" dialog allows saving multiple models into one file without combining, but it would be tedious to use that 252 times.

Command manpages:

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

> On Jun 23, 2015, at 12:44 PM, leila karami <karami.leila1 at gmail.com> wrote:
> Dear chimera users
> I have docking outputs from Swissdock (there is 252 binding modes for my ligand relative to the target protein). I used following to view my outputs:
> 1) File > Open , then load target.pdb
> 2) Tools > Surface/Binding Analysis > ViewDock, choose clusters.dock4.pdb (Dock 4, 5 or 6 format)
> Now, I want to have several pdb files in which there is target protein and each of binding modes, that is 252 pdb files. How to do this?
> Any help will highly appreciated. 

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