VMD-L Mailing List

From: Jim Pfaendtner (jpfaendt_at_hec.utah.edu)
Date: Fri Aug 24 2007 - 13:55:00 CDT

Thanks Axel,

This works exactly as you said. Now I can call vmd -args MYFILE.pdb
and then apply my saved state which now uses "$argv" as the filename.

Is there a way to further modify my saved state so that instead of
using "$argv" it will just take whatever pdb is currently on top and
apply the state to that? That way I wouldn't have to reopen VMD
every time I wanted to apply my saved state to a pdb and I could have
two pdb's open in VMD both with the applied state.

Thanks!

Jim

On Aug 22, 2007, at 12:33 PM, Axel Kohlmeyer wrote:

> On Wed, 22 Aug 2007, Jim Pfaendtner wrote:
>
>
> hi jim,
>
> i would suggest you create a matching saved state
> to your liking, then edit the filename to be read
> into a variable and then pass that filename as a
> flag when calling VMD via -args. see.
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node194.html
> and previous discussions about using -args to
> pass arguments to scripts in the mailing list archives.
>
> cheers,
> axel.
>
>
>
> JP> Dear VMD-L,
> JP>
> JP> What is the best way to automate my preferred graphic
> representation
> JP> of a protein? For example, if I am working on a particular system
> JP> with 100 residues and I always like 1-25 to be in "new
> cartoon / blue
> JP> ", 26-50 to be in "new cartoon / red" , etc. How should I go
> about
> JP> doing this? Can changes to the representation be made via a
> TCL script?
> JP>
> JP> thank you,
> JP>
> JP> Jim
> JP>
>
> --
> ======================================================================
> =
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> ======================================================================
> =
> If you make something idiot-proof, the universe creates a better
> idiot.
>