RE: [PyMOL] (no subject)
Yi,
To stuff a bunch of identical object in one PDB file, you need to assign
a unique segment ID to each one. For example:
load $PYMOL_PATH/test/dat/1tii.pdb
symexp s,1tii,1tii,5
names=cmd.get_names()
for a in range(len(names)): cmd.alter(names[a],"segi="+str(a))
save multi.pdb
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
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. mailto:war...@delsci.com
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of yi zhang
> Sent: Sunday, July 24, 2005 8:43 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
>
> Hi, everyone,
>
> I used symexp command in pymol to generate symmetry-related
> molecule, something like:
>
> cmd.symexp('sym', 'obj', 'obj',10 )
>
> of course, I can manually save each symmetry-related molecule
> to *.pdb file by clicking save molecule button, but how can I
> write a script to save all of them or part of them? the
> symmetry-related objects are not appendable.
>
> thanks!
>
> yi
>
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RE: [PyMOL] transparent sticks
Xavier,
A potentially confusing aspect of settings is that they only go down to
the object (and in some cases object-state) level. Individual atoms
don't have their own settings.
So what you've doing is changing the stick_transparency for all objects
that include atoms in the "met" selection.
The workaround is to using the "create" command to create separate
objects.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Xavier Deupi
> Sent: Wednesday, July 27, 2005 2:26 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] transparent sticks
>
> Hi,
>
> I want to set some transparency in a selection, which is
> displayed as sticks. I'm using the following command:
>
> cmd.set("stick_transparency",0.5,"ret") # where ret is the selection
>
> But when I run the script, ALL the sticks are modified, and
> not only the selection "ret", as I was expecting.
>
> I've been trying a few variations in the syntax, but I can't
> figure out the correct way... any help?
>
> Thanks in advance,
>
> Xavier
>
> --
> Xavier Deupi, Ph.D.
> Department of Molecular and Cellular Physiology Beckman
> Center for Molecular and Genetic Medicine (B161)
> 279 Campus Drive, Stanford University School of Medicine
> Stanford, CA 94305 (USA)
>
> E-mail: xavier.de...@stanford.edu
> Phone: +1 (650) 725-6497
> Fax : +1 (650) 725-8021
>
>
>
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>
Re: [PyMOL] Name length in names panel
Hello Sebastien, * Sebastien Moretti [2005-07-28 08:47] wrote: > Hello, > Is there a way to expand the names panel to be able to read object and > selection names larger than 16 characters ? At the bottom left corner of the panel, just to the left of the "VCR controls" is a little vertical bar. You can drag it to change the width of the panel. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
