VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Thu Jan 29 2009 - 15:34:31 CST

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.
>

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