VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Thu Jan 29 2009 - 19:08:08 CST

John,

>
> 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,

could you please clarify how I can add atomic element info with VMD?

> 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
>

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