Re: [PyMOL] Problematic PQS files

2005-04-28 Thread Gareth Stockwell
the address on their website. Hope that helps, Gareth --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD

Re: [PyMOL] still unresolved import pymol...

2005-04-28 Thread Gareth Stockwell
--- 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

Re: [PyMOL] Problematic PQS files

2005-04-27 Thread Gareth Stockwell
--- 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

[PyMOL] Fedora 3 problem

2005-04-21 Thread Gareth Stockwell
, 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

[PyMOL] PDB parse error?

2005-04-08 Thread Gareth Stockwell
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

Re: [PyMOL] How to apply state-specific colours?

2004-10-15 Thread Gareth Stockwell
___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome

[PyMOL] Save bug

2004-10-11 Thread Gareth Stockwell
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

[PyMOL] Save bug

2004-10-11 Thread Gareth Stockwell
(crystal) structure Sorry - definitely have my Monday head on today... Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute

Re: [PyMOL] PDB to DXF

2004-09-16 Thread Gareth Stockwell
___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute

[PyMOL] Reconstructing selections

2004-09-08 Thread Gareth Stockwell
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

Re: [PyMOL] Cavity display?

2004-07-22 Thread Gareth Stockwell
release of PyMol! Best regards, Dirk. -- Gareth Stockwell European Bioinformatics Institute

Re: [PyMOL] distance from plane

2004-07-20 Thread Gareth Stockwell
! 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

[PyMOL] CGO raytracing problem

2004-06-09 Thread Gareth Stockwell
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

Re: [PyMOL] Series of general questions

2004-04-10 Thread Gareth Stockwell
. 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

RE: [PyMOL] embeding pymol in a web page

2004-03-26 Thread Gareth Stockwell
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

[PyMOL] CGO shading

2004-03-25 Thread Gareth Stockwell
-- --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548

[PyMOL] Density sliders script

2004-03-24 Thread Gareth Stockwell
sort it out...? -- --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548

[PyMOL] Help for user-defined functions

2004-01-22 Thread Gareth Stockwell
... ''' # 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

RE: [PyMOL] H-bond drawing?

2003-11-10 Thread Gareth Stockwell
firsthand the latest developments in Apache, PHP, Perl, XML, Java, MySQL, WebDAV, and more! http://www.apachecon.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth

Re: [PyMOL] selcting water

2003-09-02 Thread Gareth Stockwell
by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute

[PyMOL] ChemPy question

2003-07-18 Thread Gareth Stockwell
/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

[PyMOL] H-bond display

2003-07-18 Thread Gareth Stockwell
, but of course I won't if it's already implemented! Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute

[PyMOL] PyMOL tutorial

2003-07-15 Thread Gareth Stockwell
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

Re: [PyMOL] coloring surfaces

2003-04-01 Thread Gareth Stockwell
@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

Re: [PyMOL] black shadows and wipe-outs

2003-03-10 Thread Gareth Stockwell
-- - 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

Re: [PyMOL] Inter-PyMOL communication?

2003-02-13 Thread Gareth Stockwell
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

Re: [PyMOL] Reading CCP4 maps

2002-09-06 Thread Gareth Stockwell
. Gareth --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548

[PyMOL] Colour by object

2002-08-15 Thread Gareth Stockwell
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

Re: [PyMOL] Re: fitting residues

2002-07-26 Thread Gareth Stockwell
://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

[PyMOL] Object-specific transparency

2002-07-25 Thread Gareth Stockwell
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

[PyMOL] Linux install problem

2002-05-03 Thread Gareth Stockwell
--- 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

[PyMOL] Fast rendering option?

2002-05-02 Thread Gareth Stockwell
the spheres when motion stops? Gareth --- Gareth Stockwell PhD student, Thornton Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD