VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Thu Apr 27 2006 - 05:06:46 CDT

hi guys,

finally i managed to finish the set of scripts for coloring of residues
in a structure according to their coordination number (number of hbonds
each residue has with its neighbors).

it allows to do the analysis, store/retrieve the results in/from a file,
average over frames and, of course, to set the user field according to
the analysis.

the code supports h-bonds going 'over the periodic boundary' (i.e., it
is fully PBC-aware).

if you are interested, you can grab it on my webpage - search for ColorCoord
http://www.molecular.cz/~vrbka/misc.html#download
i didn't want to post it on the list, since it's quite big (20k)...

john, if you would like to add it to the section with contributed
scripts on the vmd webpage, please feel free to do so.

if you find any problem/error in the scripts please let me know. i am no
tcl programmer, so the code might be sub-optimal in some cases, but it
works at the moment :)

i'd like to express my gratitude especially to john, who really helped
me a lot.

maybe this will be of some help for others.

with best regards,
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
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