VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jan 29 2009 - 20:35:35 CST

On Fri, 30 Jan 2009, Thomas Evangelidis wrote:

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

using atom selections, of course.

set sel [atomselect top "name C"]
$sel set element C

a.

TE>
TE> >or
TE> >you could load PDB files that have the atomic element info on them.
TE> >
TE> >Cheers,
TE> > John Stone
TE> > vmd_at_ks.uiuc.edu
TE> >
TE> >On Thu, Jan 29, 2009 at 11:34:31PM +0200, Thomas Evangelidis wrote:
TE> > >Dear Axel,
TE> > >
TE> > >I am trying to customize the Element representation according to my
TE> > >needs but all the atoms in my file seem to be read as "X" by VMD, as
TE> > >this is the only atomname in the Color Controls menu that alters the
TE> > >color of my molecules. Is there any way to convert my .pdb file to
TE> > >some other form that uses the VMD atom naming convention?
TE> > >
TE> > >thanks,
TE> > >Thomas
TE> > >
TE> > > >On Sun, 25 Jan 2009, Thomas Evangelidis wrote:
TE> > > >
TE> > > > TE> Dear VMD users,
TE> > > > TE>
TE> > > >
TE> > > >dear thomas,
TE> > > >
TE> > > > TE> is there any way to set the color parameters differently for
TE> > > > TE> different
TE> > > > TE> molecules. For example I want to color the carbon atoms green in
TE> > > > TE> one
TE> > > > TE> molecule and yellow in another. Can I do that in VMD?
TE> > > >
TE> > > >no. the color table is global. however you could for example
TE> > > >color different molecules with different color schemes (Name,
TE> > > >Type, Element) and thus adjust those schemes the way you like.
TE> > > >
TE> > > >
TE> > > > TE> Moreover I 'm wondering if there is any way to display H-bond
TE> > > > TE> between
TE> > > > TE> molecules from different files, or in general to make an
TE> > > >atomselection with
TE> > > >TE> atoms from different files?
TE> > > >
TE> > > >no. ... or to be more correct, not until you program it.
TE> > > >
TE> > > >cheers,
TE> > > > axel.
TE> > > >
TE> > > > TE>
TE> > > > TE> thanks in advance,
TE> > > > TE> Thomas
TE> > > > TE>
TE> > > >
TE> > > >--
TE> > > >=======================================================================
TE> > > >Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
TE> > > > Center for Molecular Modeling -- University of Pennsylvania
TE> > > >Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
TE> > > >tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
TE> > > >=======================================================================
TE> > > >If you make something idiot-proof, the universe creates a better idiot.
TE> > > >
TE> > >
TE> > >
TE> > >----- End message from akohlmey_at_cmm.chem.upenn.edu -----
TE> > >
TE> > >
TE> >
TE> >--
TE> >NIH Resource for Macromolecular Modeling and Bioinformatics
TE> >Beckman Institute for Advanced Science and Technology
TE> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
TE> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
TE> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
TE> >
TE>
TE>
TE> ----- End message from johns_at_ks.uiuc.edu -----
TE>
TE>
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.