From: Jim Kress (jimkress_58_at_kressworks.org)
Date: Thu Aug 09 2012 - 13:26:28 CDT

Thanks Axel.

Jim

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf Of Axel Kohlmeyer
> Sent: Thursday, August 09, 2012 12:13 PM
> To: Jim Kress
> Cc: vmd-l_at_ks.uiuc.edu; John Stone
> Subject: Re: vmd-l: unique residue names
>
> On Thu, Aug 9, 2012 at 4:55 PM, Jim Kress <jimkress_58_at_kressworks.org>
> wrote:
> > I'll probably get a RTFM from Axel on this :>} , but I couldn't
figure
> > out how to do it so I'll ask the community.
> >
> >
> >
> > I have a pdb trajectory file in which I have created my own unique
> "residue"
> > names (e.g. AAA, AAB, AAC, etc.). I have a variety of the "residue"
> > names and I would like to set the display so I can assign specific
> > display attributes to each "residue" (e.g. ball and stick to AAA,
> > lines to AAB, vdw to AAC, the color red to AAA, blue to AAB, green to
AAC,
> etc.).
>
> > How do I do this with VMD 1.9.1?
>
> similar problems have been discussed
> on this mailing list in the past and in principle it is all described in
the user's
> guide in one way or another. however, here is a strategy that should work
> even for people that only want to learn a minimal amount of VMD scripting:
>
> load your file
> build your various visualizations
> save this state to a file and load
> it into a text editor.
>
> delete everything from the beginning up to and including the line starting
> with "mol new"
>
> and then delete everything until the end starting from and including the
line
> starting with "mol rename".
>
> save this file to "myviz.vmd"
>
> in principle, you could trim this file down even more by keeping only:
>
> mol delrep 0 top
>
> and all lines with:
>
> mol representation <...>
> mol color <...>
> mol selection <...>
> mol material <...>
> mol addrep top
>
> once you have this. load a new file
> and then do "play myviz.vmd"
> and you are done.
>
> if you want to automate this even more,
> have a look at this hack:
> http://sites.google.com/site/akohlmey/random-hacks/vmd-initialization-
> scripts#TOC-Custom-Actions-at-Molecule-Load
>
> enjoy,
> axel.
>
>
> >
> >
> > Thanks.
> >
> >
> >
> > Jim
> >
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International
> Centre for Theoretical Physics, Trieste. Italy.