VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Oct 20 2007 - 14:00:02 CDT

On Sat, 20 Oct 2007, Sanghyun Park wrote:

SP> Hi John and Axel -

dear sangyun,
 
SP> I'm not trying to accomplish anything. I just don't like seeing all
SP> the X's VMD put in my PDB; it makes me dizzy. If there is no simple

well, but it is a field required by the PDB standard.
if you check the definition of ATOM records in the PDB
standard format documentation, only charge and sequence
entries are named optional.

axel.

SP> way within VMD, I'll just write a little script to remove all the X's
SP> in the chain column. (I'll call it "X-killer".)
SP>
SP> Thanks!
SP> Sanghyun
SP>
SP> On 10/19/07, John Stone <johns_at_ks.uiuc.edu> wrote:
SP> >
SP> > Hi Sanghyun,
SP> > The existing VMD code won't allow a blank chain ID, which is why
SP> > it auto-assigns "X" if one is not otherwise set. If you want to change
SP> > that behavior, I can probably send you a patch, but without knowing
SP> > what you're trying to accomplish, changint that detail may not help much.
SP> > If you can tell me what you're attempting to accomplish, I can help you
SP> > get it done.
SP> >
SP> > Cheers,
SP> > John Stone
SP> > johns_at_ks.uiuc.edu
SP> >
SP> > On Fri, Oct 19, 2007 at 09:57:10PM -0500, Sanghyun Park wrote:
SP> > > Hi,
SP> > >
SP> > > How can I remove the chain id "X" automatically assigned by VMD? I've tried
SP> > >
SP> > > set all [atomselect top "all"]
SP> > > $all set chain " "
SP> > >
SP> > > But, that doesn't seem to work.
SP> > >
SP> > > Thanks,
SP> > > Sanghyun
SP> >
SP> > --
SP> > NIH Resource for Macromolecular Modeling and Bioinformatics
SP> > Beckman Institute for Advanced Science and Technology
SP> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
SP> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
SP> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
SP> >
SP> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.