VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 29 2009 - 15:41:18 CST

Thomas,
  The 'element' field in VMD is populated only by PDBs that contain
atomic element symbol text on the right hand side of the ATOM records.
PDB files that don't contain element info aren't automatically
"guessed" at present, so they are assigned as element "X".
You can write atom selections to either fix them manually, or
you could load PDB files that have the atomic element info on them.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 29, 2009 at 11:34:31PM +0200, Thomas Evangelidis wrote:
> Dear Axel,
>
> I am trying to customize the Element representation according to my
> needs but all the atoms in my file seem to be read as "X" by VMD, as
> this is the only atomname in the Color Controls menu that alters the
> color of my molecules. Is there any way to convert my .pdb file to
> some other form that uses the VMD atom naming convention?
>
> thanks,
> Thomas
>
> >On Sun, 25 Jan 2009, Thomas Evangelidis wrote:
> >
> >TE> Dear VMD users,
> >TE>
> >
> >dear thomas,
> >
> >TE> is there any way to set the color parameters differently for different
> >TE> molecules. For example I want to color the carbon atoms green in one
> >TE> molecule and yellow in another. Can I do that in VMD?
> >
> >no. the color table is global. however you could for example
> >color different molecules with different color schemes (Name,
> >Type, Element) and thus adjust those schemes the way you like.
> >
> >
> >TE> Moreover I 'm wondering if there is any way to display H-bond between
> >TE> molecules from different files, or in general to make an
> >atomselection with
> >TE> atoms from different files?
> >
> >no. ... or to be more correct, not until you program it.
> >
> >cheers,
> > axel.
> >
> >TE>
> >TE> thanks in advance,
> >TE> Thomas
> >TE>
> >
> >--
> >=======================================================================
> >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.
> >
>
>
> ----- End message from akohlmey_at_cmm.chem.upenn.edu -----
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078