VMD-L Mailing List

From: Axel Berg (axel_at_sara.nl)
Date: Fri Mar 05 1999 - 06:38:48 CST

Hi,

I have been playing around with the MSMS surface calculation option of VMD,
which is much faster and convenient than the normal rather slow surface option
of VMD. However, I encountered the following problem with MSMS: if the atom
selection does not start from residue one (or at least the first residue in the
pdb file), colouring of atoms on the MSMS surface is wrong. So for example when
you select resid 2 to 20 and use as representation MSMS, and color according to
restype, name or something else that uses different colors for atoms, the
colouring is not right. If you select the complete protein, or select e.g.
resid 1 to 20, the colouring for the MSMS surface is right. So it seems like
the atomlist array for colouring the MSMS surface is somehow wrong and starts
always from the first atom of the pdb file and not from the first atom of the
particular selection. When using the normal (slow) surface (surf), there is
never a problem.

Does anyone know about this problem, and does anyone know a way to fix this?

I would very much like a solution to this problem, since I use the surface
option quite often, and I like MSMS because of its superior speed.

The second question I have concerns H-bonds. Does anyone know a way to write
the H-bonds (partners), that VMD determines and shows on the screen, to a file?

Thanks in advance,

Kind regards,

Axel 

--
        Axel Berg
        SARA - Academic Computing Services Amsterdam 
        Kruislaan 415
        1098 SJ Amsterdam 
        The Netherlands 
        Phone: +31 20 592 3000 
        Fax:   +31 20 668 3167
        URL:   http://www.sara.nl 
        email: axel_at_sara.nl