VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 09 2012 - 11:12:39 CDT
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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.
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