VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Aug 24 2007 - 13:08:44 CDT

On Fri, 24 Aug 2007, Jim Pfaendtner wrote:

hi jim,

JP> Thanks Axel,
JP>
JP> This works exactly as you said. Now I can call vmd -args MYFILE.pdb
JP> and then apply my saved state which now uses "$argv" as the filename.
JP>
JP> Is there a way to further modify my saved state so that instead of
JP> using "$argv" it will just take whatever pdb is currently on top and
JP> apply the state to that? That way I wouldn't have to reopen VMD
JP> every time I wanted to apply my saved state to a pdb and I could have
JP> two pdb's open in VMD both with the applied state.

for that purpose you can use the clonereps plugin. this will
clone the representation of a given molecule onto one or multiple
other molecules that are currently loaded into VMD. it also works
on the script level, if needed.

cheers,
   axel.

JP>
JP> Thanks!
JP>
JP> Jim
JP>
JP> On Aug 22, 2007, at 12:33 PM, Axel Kohlmeyer wrote:
JP>
JP> > On Wed, 22 Aug 2007, Jim Pfaendtner wrote:
JP> >
JP> >
JP> > hi jim,
JP> >
JP> > i would suggest you create a matching saved state
JP> > to your liking, then edit the filename to be read
JP> > into a variable and then pass that filename as a
JP> > flag when calling VMD via -args. see.
JP> > http://www.ks.uiuc.edu/Research/vmd/current/ug/node194.html
JP> > and previous discussions about using -args to
JP> > pass arguments to scripts in the mailing list archives.
JP> >
JP> > cheers,
JP> > axel.
JP> >
JP> >
JP> >
JP> > JP> Dear VMD-L,
JP> > JP>
JP> > JP> What is the best way to automate my preferred graphic
JP> > representation
JP> > JP> of a protein? For example, if I am working on a particular system
JP> > JP> with 100 residues and I always like 1-25 to be in "new
JP> > cartoon / blue
JP> > JP> ", 26-50 to be in "new cartoon / red" , etc. How should I go
JP> > about
JP> > JP> doing this? Can changes to the representation be made via a
JP> > TCL script?
JP> > JP>
JP> > JP> thank you,
JP> > JP>
JP> > JP> Jim
JP> > JP>
JP> >
JP> > --
JP> > ======================================================================
JP> > =
JP> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
JP> > www.cmm.upenn.edu
JP> > Center for Molecular Modeling -- University of Pennsylvania
JP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
JP> > 19104-6323
JP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
JP> > ======================================================================
JP> > =
JP> > If you make something idiot-proof, the universe creates a better
JP> > idiot.
JP> >
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.