[PyMOL] neighbor selection
Hi there,
I have bunch of structures in the session but only one of them (molA)
displayed.
I'm trying to select atoms within a given radius from my point of interest.
When I do
select cont,(/molA//s/401 around 4)
it sure selects all atoms from molA that are within 4 A from residue 401 but
it also selects
ALL other atoms from the current session (but not displayed) that are within
4 A.
What needs improvement - the program or my command?
Cheers,
n.
Ruslan Sanishvili (Nukri) Ph.D.
GM/CA-CAT, ANL
9700 S. Cass Ave.
Argonne, IL 60439
Tel (630)252-0665
Fax (630)252-0667
rsanishv...@anl.gov
- Original Message -
From: "Robert Campbell"
To:
Sent: Thursday, February 06, 2003 9:00 AM
Subject: Re: [PyMOL] nice povray settings?
> Oooops
>
> I [2003-02-05 11:42] wrote:
> >
> > I typically use the following script (I call it make_pov.py) and
> > "run" it from pymol once to load the function, and then I do
> > "make_pov('povray.inp')" to create the povray.inp file.
>
> But of course I forgot to include the script, which is very short:
>
> # make_pov.py
> # Do "run make_pov.py" from within pymol and then execute the script
> # with "make_pov('povray.inp')" to create the povray.inp file.
> #
> from pymol import cmd
>
> def make_pov(file):
> (header,data) = cmd.get_povray()
> povfile=open(file,'w')
> povfile.write(header)
> povfile.write(data)
> povfile.close()
>
>
> Cheers,
> Robert
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associatephone: 613-533-6821
> Dept. of Biochemistry, Queen's University, fax: 613-633-2497
> Kingston, ON K7L 3N6 Canada
> PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
> (out of date web site:http://biophysics.med.jhmi.edu/rlc)
>
>
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RE: [PyMOL] Pymol and Autodock
SD is a file format for small molecule ligands based around the MDL MOL file (CTAB core). http://www.mdli.com/downloads/literature/ctfile.pdf Advantages: simplicity easy to parse supported by most cheminformatics packages captures valence, stereochem, charge 2D or 3D more extensible than PDB (arbitrary tags) Disadvantages: 999 atom limit (only useful for small molecules!) no standard conventions for storing of atom names or types. fixed field lengths Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -Original Message- > From: Alan Wilter Sousa da Silva [mailto:a...@biof.ufrj.br] > Sent: Thursday, February 06, 2003 7:41 AM > To: DeLano, Warren > Cc: Chris; PyMOL-users > Subject: Re: [PyMOL] Pymol and Autodock > > > > On Thu, 6 Feb 2003, Warren L. DeLano wrote: > > > Read-in performace would be better if you could convert your > > multiligand PDB file to an SD file. > > Sorry, what's SD? > > TIA, > Cheers, > > --- > Alan Wilter S. da Silva > --- > Laboratório de Física Biológica > Instituto de Biofísica Carlos Chagas Filho >Universidade do Brasil/UFRJ > Rio de Janeiro, Brasil > >
Re: [PyMOL] Pymol and Autodock
On Thu, 6 Feb 2003, Warren L. DeLano wrote: > Read-in performace would be better if you could convert your > multiligand PDB file to an SD file. Sorry, what's SD? TIA, Cheers, --- Alan Wilter S. da Silva --- Laboratório de Física Biológica Instituto de Biofísica Carlos Chagas Filho Universidade do Brasil/UFRJ Rio de Janeiro, Brasil
Re: [PyMOL] Pymol and Autodock
On Thu, 6 Feb 2003, Chris wrote: > A couple of quick questions for anyone running Pymol and Autodock. > 1. Doing Get dockings in autodock writes out a PDB formatted file, and uses > the ` MODEL ' and ` ENDMDL ' records to denote the different dockings is > there anyway to get pymol to read these as individual "states" ? - If not PyMOL does support the MODEL and ENDMDL tags, but so far they've only been tested with NMR structures (as far as I know). With different ligands in one PDB file, it may be necessary to force PyMOL treat each state as a separate entity using the "discrete=1" flag. load ligands.pdb,discrete=1 Unfortunately, reading of MODEL and ENDMDL records is not (yet) optimized, so this might bog down. Read-in performace would be better if you could convert your multiligand PDB file to an SD file. > does anyone know of a program that will read these files (other than > autodock tools (For some reason Autodocktools comes back with strange OpenGl > errors (very odd seen as Pymol works great on my wee linux box)) . > 2. Is there anyway to directly import Trajectory files (.trj) from simulated > annealing dockings into Pymol ? for doing animations in Pymol No, but you might be able to use PyMOL's "chempy" models to create your own (depending on how easy/hard it would be to read ".trj" files in Python. Warren
Re: [PyMOL] nice povray settings?
Oooops
I [2003-02-05 11:42] wrote:
>
> I typically use the following script (I call it make_pov.py) and
> "run" it from pymol once to load the function, and then I do
> "make_pov('povray.inp')" to create the povray.inp file.
But of course I forgot to include the script, which is very short:
# make_pov.py
# Do "run make_pov.py" from within pymol and then execute the script
# with "make_pov('povray.inp')" to create the povray.inp file.
#
from pymol import cmd
def make_pov(file):
(header,data) = cmd.get_povray()
povfile=open(file,'w')
povfile.write(header)
povfile.write(data)
povfile.close()
Cheers,
Robert
--
Robert L. Campbell, Ph.D.
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-633-2497
Kingston, ON K7L 3N6 Canada
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
(out of date web site:http://biophysics.med.jhmi.edu/rlc)
[PyMOL] Pymol and Autodock
Hi Guys A couple of quick questions for anyone running Pymol and Autodock. 1. Doing Get dockings in autodock writes out a PDB formatted file, and uses the ` MODEL ' and ` ENDMDL ' records to denote the different dockings is there anyway to get pymol to read these as individual "states" ? - If not does anyone know of a program that will read these files (other than autodock tools (For some reason Autodocktools comes back with strange OpenGl errors (very odd seen as Pymol works great on my wee linux box)) . 2. Is there anyway to directly import Trajectory files (.trj) from simulated annealing dockings into Pymol ? for doing animations in Pymol Cheers in advance Chris
Re: [PyMOL] running pymol in command mode
Dear Matt, There is a straighter way to do it. Try just pymol.com pymol_script.pml (This works at least on my Linux machine). You can also try cat pymol_script.pml | pymol.com -p or even tail -f pymol_script.pml | pymol.com -p The latter allows one to append lines to the pymol script from an external program, which will be executed immediately. Kristian > I'm trying to use pymol to render a large number of complex images in > order to make a molecular movie. .. > > However, I'm having trouble getting the command mode to function. It > appears that one should launch pymol like so: > > pymol.com -c < pymol_script > > where "pymol_script" is a script file that you could otherwise invoke > from the GUI's command line by "@pymol_script". However, when I try > this with a simple script like:
