VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Fri Oct 21 2005 - 11:15:40 CDT

 When I have to screen a number of docked protein complexes (using VMD under WinXP), I like to write a short script that loads the complex and automatically creates representations for the areas of interest, e.g. CPK for some critical residues and Tube for the rest. You can keep the script open in e.g. WordPad, and just change the filename, save, and Source the script from VMD. If your filenames are something of the form XXX001.pdb, XXX002.pdb, etc., then this is especially easy.

# Load PDB-format complex
mol new "Complex_57g.pdb"
# Create tube representation of backbone
mol modstyle 0 top Tube
# Add representation to molecule 0
mol addrep top
# Change to CPK representation
mol modstyle 1 top CPK
# Limit selection of CPK representation (1) of molecule 0 to the desired selection.
mol modselect 1 top "(chain A and resid 111 166 366 370) or (chain B and resid 69 74 77 107)"

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Björn Windshügel
> Sent: Friday, October 21, 2005 8:55 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Loading multiple molecules in one step /
> "Apply changes automatically"
>
> Hi everybody,
>
> can anyone tell me if there is a possibility in VMD to load
> more than one molecule in a step? When analysing docking
> results it sucks loading 40 docked conformations using the
> standard procedure. It would be nice having the possibility
> to load the content of a whole directory or to select several
> files at once for example by using the Shift or Strg Key.
>
> Another observation is that having done a selection for a
> trajectory using the command "within 5 of resid 333" and
> having clicked "Apply changes automatically" I always have to
> click the "Apply" button when watching another frame since
> the changes are not done automatically. In a previous version
> of VMD (1.6 or so) this worked fine.
>
> Best regards,
>
> Björn
>
>
>
> --
> Björn Windshügel
> Institut für Pharmazeutische Chemie phone: (49)345 55-25043
> Martin-Luther-Universität Halle-Wittenberg fax: (49)345 55-27355
> Wolfgang-Langenbeck-Strasse 4 web:
> www.drugdesigner.de
> 06114 Halle (Saale)
>