[Chimera-users] find the region around a volume imported from 3V voxelator

Fabian Glaser fglaser at technion.ac.il
Thu Sep 9 11:26:05 PDT 2010

Daer chimera team,
I am interested in finding a channel in a toluene hydrogenase, and
extracting all the residues / atoms surrounding this channel. To do
that I calculated the channel itself using the 3V voxelator
(http://3vee.molmovdb.org), which produces a volume object that can be
imported to chimera. See for example the output page
http://3vee.molmovdb.org/viewResults.php?jobid=10sep02.ee6, which
provides the file channel-004.mrc.gz, which needs to be first
unzipped. When uploaded to chimera the volume is very clear and nice.

But I want to find the residues/ atoms that form the channel, one the
pdb itself 3DHG.pdb.gz, although the select and zone features seem to
not work with the volume object.

Any idea how to do that?

Thanks a lot,

Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

E-mail: fglaser at technion.ac.il
Tel:    +972-4-8293701
Fax:   +972-4-8225153

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