Re: writing back coordinates of waters that cross the unit cell

From: Nicholas M Glykos (
Date: Thu Nov 25 2010 - 09:53:19 CST

> For further work I wold like to cut out different water spheres around the
> protein from a snapshot, So I would need a buffer of water around the
> protein.

Thomas Evangelidis had once upon a time written a VMD script (named
'trunctraj') which was supposed to apply PBC translations in order to
generate a new DCD file containing a specified number of waters around the
protein component. The script is still there (in something like
/usr/local/lib/vmd/plugins/noarch/tcl/trunctraj1.5/) _but_ I have never
used it and (obviously) can not promise that it will do the trick.


          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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