[PyMOL] fill a cavity with a closed polygon

? -- Jed Goldstone Visting Investigator Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.mit.edu/people/jedgold/home.html (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI)

[PyMOL] pymol autodock plugin

Numeric Error: unable to initialize plugin 'autodock'. Any help would be greatly appreciated. Jed -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32

[PyMOL] Autodock/Vina Pymol Plugin Windows problem

-- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's

Re: [PyMOL] coordinates

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jed Goldstone

Re: [PyMOL] coordinates

. Apologies to the list, Jed Robert Campbell wrote: Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote: Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid

Re: [PyMOL] PC based docking program!

-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution

Re: [PyMOL] some help

-users@lists.sourceforge.net -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823

[PyMOL] using pymol on a remote server

unfamiliar with this, and do not know how to implement it (my desktop runs PyMol 1.2r1 on Windows XP). Would this be an appropriate solution? Would it work to call remote plugins? Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Woods

Re: [PyMOL] CASTp plugin

\startup\CASTpyMOL_v2.pyc Error: unable to initialize plugin 'CASTpyMOL_v2'. Does anyone have any idea how to fix this issue? Thanks, Tomas -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543

Re: [PyMOL] Logging the sculpt wizard

You might want to try using Modeller instead. http://www.salilab.org/modeller/wiki/Mutate%20model It does higher level modelling. Jed Martin Hediger wrote: Dear List I'm trying to automate the following sequence of steps in a PyMOL python script: 1. Start the mutagenesis wizard 2. Mutate a

Re: [PyMOL] RMSD calculation sans alignment

/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jed Goldstone, PhD

Re: [PyMOL] Set values for dihedral angles

James- I think you need to seriously consider using software that's actually designed to compute and refine protein models, such as Modeller. There are forcefield and structural constraints that PyMol is just not designed to do, and your results may not have the scientific validity you

[PyMOL] Caver 3.01 with Pymol 1.6.0.0 on Windows 7

)) File C:\Program Files\PyMOL\PyMOL/modules\pmg_tk\startup\Caver3_0_1.py, line 638, in loadFileContent handler = open(file) type 'exceptions.IOError': [Errno 2] No such file or directory: 'C:/Users/Jed/modeling/caver/caver_output/2/warnings.txt' -- Jed

Re: [PyMOL] How to automate RMSD calculation for large no of structures

-users@lists.sourceforge.net -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823

[PyMOL] combining multiple objects into one multistate object

up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32

Re: [PyMOL] combining multiple objects into one multistate object

end Cheers, -- Jason On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu mailto:jgoldst...@whoi.edu wrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded

Re: [PyMOL] Pymol Mobile viewer?

body, registered in Scotland, with registration number SC005336. -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823

Re: [PyMOL] coloring based on alignment

Vaheh, You can modify the b-factor column, and color by b-factor. I have used various value-to-bfactor scripts, with different measures of alignment similarity. The one problem I've had is extending the Ca color to the rest of the residue in stick mode. Jed On Oct 28, 2015 3:34 PM, "Oganesyan,

Re: [PyMOL] electrostatic potential as cartoon?

Vincent, You could use data2bfactor.py and then "spectrum b" to color residues in cartoon settings. https://pymolwiki.org/index.php/Color (data2bfactor from Robert Campbell's script repository: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Jed On 1/4/2017 11:05 AM, vincent Chaptal

Re: [PyMOL] (no subject)

rceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- - Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Instit