RE: [PyMOL] distance between aromatic residues

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

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

idcswdc.com/cgi-bin/survey?id5hix > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > --- Gar

Re: [PyMOL] Problematic PQS files

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

Re: [PyMOL] Problematic PQS files

__ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > --- Gareth Stockwell EMBL - European Bioinforma

[PyMOL] Fedora 3 problem

, 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

RE: [PyMOL] PDB parse error?

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

[PyMOL] PDB parse error?

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

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

us > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourcefo

[PyMOL] Save bug

the remaining (crystal) structure Sorry - definitely have my Monday head on today... Gareth -- Gareth Stockwell European Bioinformatics Institute

[PyMOL] Save bug

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

Re: [PyMOL] PDB to DXF

; Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell European Bioinformatics Institute

[PyMOL] Reconstructing selections

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

Re: [PyMOL] Cavity display?

would be my wish for a next > release of PyMol! > > Best regards, > > Dirk. -- Gareth Stockwell European Bioinformatics Institute

Re: [PyMOL] distance from plane

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

[PyMOL] CGO raytracing problem

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

Re: [PyMOL] Series of general questions

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 -- -------

RE: [PyMOL] CGO shading

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 > >

RE: [PyMOL] embeding pymol in a web page

'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

[PyMOL] CGO shading

1.2 Mesa 4.0.4 Cheers, Gareth -- ------- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar.

Re: [PyMOL] Density sliders script

d which does the job for now. Hope this is useful, Gareth -- Gareth Stockwell European Bioinformatics Institute

[PyMOL] Density sliders script

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

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

RE: [PyMOL] H-bond drawing?

bDAV, and more! http://www.apachecon.com/ > _______ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell European Bioinformatics Institute

Re: [PyMOL] selcting water

> > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.n

[PyMOL] H-bond display

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

RE: [PyMOL] H-bond display

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

RE: [PyMOL] H-bond display

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

[PyMOL] H-bond display

course I won't if it's already implemented! Gareth -- Gareth Stockwell European Bioinformatics Institute

[PyMOL] ChemPy question

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

[PyMOL] PyMOL tutorial

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] Drawing dashed lines

__ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- --- Gareth Stockwel

Re: [PyMOL] coloring surfaces

/go/sdnxxaff00300020aff/direct/01/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- -

Re: [PyMOL] black shadows and wipe-outs

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

Re: [PyMOL] Inter-PyMOL communication?

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:

[PyMOL] Inter-PyMOL communication?

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

Re: [PyMOL] Using DSSP output

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

Re: [PyMOL] Reading CCP4 maps

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

[PyMOL] Transparent spheres

suggestions, Gareth -- - Gareth Stockwell PhD student, Thornton Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar

[PyMOL] Colour by object

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

[PyMOL] Colour by object

-- - 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

Re: [PyMOL] Re: fitting residues

ber.com/osdn/xim > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > --- Gareth Stockwell Ph

[PyMOL] Object-specific transparency

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

[PyMOL] Suggestions

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

[PyMOL] Linux install problem

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

[PyMOL] Fast rendering option?

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