the spheres when
motion stops?
Gareth
---
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
---
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548 http
objects behave in the same way as the
molecule objects?
Gareth
--
-
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
://lists.sourceforge.net/lists/listinfo/pymol-users
---
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
in a
molecule differently)? This would be really useful in visualising a
set of superposed structures.
The script is also available at
http://www.ebi.ac.uk/~gareth/misc
Gareth
--
-
Gareth Stockwell
PhD student
.
Gareth
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548
to have
a master/slave setup.
Jules
On 13 Feb 2003, Gareth Stockwell wrote:
Is there any way to have more than one PyMOL session respond to the same
user input? What I would like to do is the following:
Have several PyMOL windows open side-by-side, each containing a
different
--
-
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
gar...@ebi.ac.uk
Tel (+44) 01223 492548
http://www.ebi.ac.uk/~gareth
@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
-
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
encoder.
You can find both of them at
http://www.ebi.ac.uk/~gareth/work/pymol
Gareth
--
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
/x.pdb)
cmd.load_object(8,m,protein)
make_atom_sel(my_sel, [0,2,5,8,18,22], m, protein)
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
, but
of course I won't if it's already implemented!
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
by:ThinkGeek
Welcome to geek heaven.
http://thinkgeek.com/sf
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--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
firsthand the latest
developments in Apache, PHP, Perl, XML, Java, MySQL,
WebDAV, and more! http://www.apachecon.com/
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--
Gareth
...
'''
# Python code here...
cmd.extend(some_func, some_func)
#--
... and then type 'help some_func'.
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
sort it out...?
--
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548
--
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548
not sure about the licence position on the EBI version though; if
you're interested, I'm sure someone from the MSD group could help out.
Gareth
--
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust
. For
example,
select all_oxygen, (e;o)
select backbone_oxygen, (n;o)
So to select sidechain atoms of an existing selection my_sel:
select sidechain_of_my_sel, (my_sel !n;n,c,o)
Gareth
--
---
Gareth Stockwell
EMBL
normals are the problem - do I need to compute
and then explictly state a normal for each vertex?
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
from pymol.cgo import *
from pymol import cmd
conservation_3_surf_cgo = [ BEGIN, TRIANGLES,
COLOR, 0, 1, 0.317521
!
Is there a way for me to define a plane of atoms say 4 Nitrogens in a heme
complex and then determine how far out-of-plane the Fe atom is? If so
either in Pymol or another program I'd love to know the secret.
Thanks,
Kristl
kri...@physics.purdue.edu
--
Gareth Stockwell gar...@ebi.ac.uk
release of PyMol!
Best regards,
Dirk.
--
Gareth Stockwell
European Bioinformatics Institute
order that they appear in the PDB file?
ii) If so, is there any way to directly construct a selection containing
e.g. atoms 1,3,8,10,11... of a given object?
... and of course any other comments or advice are most welcome!
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics
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--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
Using 0.98beta05 on Linux, the 'save' command does not work. Doing
either of
save some_filename.pdb
save some_filename.pdb, an_object
just produces a file containing END.
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
(crystal) structure
Sorry - definitely have my Monday head on today...
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
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---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome
Warren,
Using version 0.97, if I load a PDB with an atom like this:
HETATM 2051 N A HEM B 400 -7.209 4.751 30.974 1.00
16.78 N
(e.g. in PDB 1f1c)
Then Pymol loads the atom name as 'N' rather than 'N A'. Is there a way
around this?
Gareth
--
Gareth Stockwell gar
, but
they are the same as the ones bundled with FC3. When I tried installing
them after the OS, I got exactly the same problem.
http://www.ebi.ac.uk/~gareth/pymol/fc3_problem
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548 http://www.ebi.ac.uk
the address on their website.
Hope that helps,
Gareth
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548 http://www.ebi.ac.uk/~gareth
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