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

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
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.

Nicholas

-- 
          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, http://utopia.duth.gr/~glykos/

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