tions are fast, then re-render the spheres when
motion stops?
Gareth
-------
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campu
7;t have root access on this system
-------
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
First let me say that PyMol is the most useful and powerful open-source
software I have come across.
I am running the 0.78 version, installed from RPM onto a RedHat Linux
7.3 system with an nVidia Vanta graphics card.
I have a few comments:
1. There appears to be a bug in the isomesh routine (s
B'.
Is there a way to make isosurface objects behave in the same way as the
molecule objects?
Gareth
--
-----
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust
ber.com/osdn/xim
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Gareth Stockwell
Ph
--
-
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
gar...@ebi.ac.uk
Tel 01223 492548Personal homepage:
http
r each chain 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 St
suggestions,
Gareth
--
-
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
gar
.
Gareth
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548
ing list
> PyMOL-users@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
gar...@ebi.ac.uk
Tel 01223 492548Personal homepage:
http://www.ebi.ac.uk/~gareth
was designated the
'master', and all commands executed on that session were piped to each
of its 'slaves'?
Gareth
--
---------
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Ge
open and wouldn't need 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:
ing list
> PyMOL-users@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
/go/sdnxxaff00300020aff/direct/01/
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Gareth Stockwel
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
two functions, the program I
execute in order to reconstitute my molecule in PyMOL looks like
m = io.pdb.fromFile("/tmp/x.pdb")
cmd.load_object(8,m,"protein")
make_atom_sel("my_sel", [0,2,5,8,18,22], m, "protein")
Gareth
--
Gareth Stockwell
European Bioinformatics Institute
course I won't if it's already implemented!
Gareth
--
Gareth Stockwell
European Bioinformatics Institute
Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> > ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell
> > Sent: Friday, July 18, 2003 2:46
On Fri, 2003-07-18 at 18:25, Warren L. DeLano wrote:
> Gareth,
>
> cmd.identify returns the input indexing, which will correspond
> to the PDB file.
>
> cmd.index returns the internal indexing, which will correspond
> to cmd.get_model
>
> help identify
&g
names aren't supplied
The new version, with correct indenting, is available for download at
http://www.ebi.ac.uk/~gareth/work/pymol
Gareth
--
Gareth Stockwell
European Bioinformatics Institute
>
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> Welcome to geek heaven.
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Gareth Stockwell
European Bioinformatics Institute
Some help docs here...
'''
# Python code here...
cmd.extend("some_func", some_func)
#--
... and then type 'help some_func'.
Gareth
--
Gareth Stockwell
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
d which does the job for now. Hope this is
useful,
Gareth
--
Gareth Stockwell
European Bioinformatics Institute
1.2 Mesa 4.0.4
Cheers,
Gareth
--
-------
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar.
'm 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 Bioinformatic
y PyMOL page (it's called walls.py)
http://www.ebi.ac.uk/~gareth/pymol/
Gareth
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > Gareth Stockwell
> >
e.
PyMOL distinguished between element types and PDB atom names. 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
--
-------
normals are the problem - do I need to compute
and then explictly state a normal for each vertex?
Gareth
--
Gareth Stockwell
European Bioinformatics Institute
from pymol.cgo import *
from pymol import cmd
conservation_3_surf_cgo = [ BEGIN, TRIANGLES,
COLOR, 0, 1, 0.317521,
VERTEX, -8.5, -1.5
Adams wrote:
> Hi Pymolers!
>
> 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
would be my wish for a next
> release of PyMol!
>
> Best regards,
>
> Dirk.
--
Gareth Stockwell
European Bioinformatics Institute
guarantee that atoms are stored internally in the same
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
European Bioinformatics Institute
; Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
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Gareth Stockwell
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
European Bioinformatics Institute
the remaining (crystal) structure
Sorry - definitely have my Monday head on today...
Gareth
--
Gareth Stockwell
European Bioinformatics Institute
us
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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
50)-346-1154
> . mailto:war...@delsci.com
>
>
> > -Original Message-----
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > Gareth Stockwell
> > Sent: Friday, April 08, 2005 6
, 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
European Bioinformatics Institute
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>
---
Gareth Stockwell
EMBL - European Bioinforma
ill be 100% correct)
If you want to know more details, I'd suggest you contact the MSD team via
the address on their website.
Hope that helps,
Gareth
---
Gareth Stockwell
EMBL - Euro
idcswdc.com/cgi-bin/survey?id5hix
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>
---
Gar
On Tue, 2005-05-24 at 11:34 +0200, Grégori Gerebtzoff wrote:
> 3) define two interlaced loops and calculate the distance between all 6
> carbons of Phe1 with all 6 carbons of Phe2, either with cmd.dist or with
> simple mathematical functions; sum these distances
>
> 4) divide the result by 36, and
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