Robert,
Great point! My original script had selections from protein A to a
ligand in any other protein B. I just left it in there.
I agree that creating a named selection for each object is
unnecessary. If he really wanted a clean namespace, he could dump all
of those into a group(s) or a multi-state object.
Nice attention to detail,
-- Jason
--
Jason Vertrees, PhD
PyMOLWiki -- http://www.pymolwiki.org
On Sun, Nov 29, 2009 at 9:50 PM, Robert Campbell
robert.campb...@queensu.ca wrote:
Hi Jason,
On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees jason.vertr...@gmail.com
wrote:
You can automate the task. Load your 100 proteins. Use a wildcard
from the command line or a script like loadDir
(http://pymolwiki.org/index.php/LoadDir). Align them. Then, run:
python
for n in cmd.get_names(objects):
selName = s + n
cmd.select(selName, n)
cmd.distance(dist+n, selName, selName + and (organic and + n + ),
3.2, mode=2)
python end
I'm just curious, but why do you go to the trouble to create a selection that
is just the whole object? Especially if Chimed has 100s of objects, he
doesn't need to add a named selection for each. Why not do the following?
python
for n in cmd.get_names(objects):
cmd.distance(dist+n,n,n + and organic,3.2, mode=2)
python end
The latter worked for me. If you wanted to eliminate waters from
the selection for the protein, you could change it to:
python
for n in cmd.get_names(objects):
cmd.distance(dist+n,n + and not solvent,n + and organic,3.2,mode=2)
python end
Or to make it more readable:
python
for n in cmd.get_names(objects):
protein_sele = n + and not solvent
organic_sele = n + and organic
cmd.distance(dist+n, protein_sele, organic_sele, 3.2, mode=2)
python end
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc
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