[PyMOL] Problem with ribbon

lick on the endpoints (to see the residue number) The one that should be 25, displays residue 20. Labels do show the correct residue numbers. Mark ___ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB

[PyMOL] 1.7.6.6 does not display a 1.7.4.4 .pse ifle.

?_scene_" + key + "_" + rep_name) File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/viewing.py", line 593, in show if _self._raising(r,_self): raise QuietException pymol.parsing.QuietException: Suggestions? Do you want to examine the f

[PyMOL] Improve scene command?

On the wiki page for scene, it states: DEVELOPMENT TO DO Add support for save/restore of a certain global and object-and-state specific settings, such as: state, surface_color, ribbon_color, stick_color, transparency, sphere_transparency, etc. This would probably best be done by defining a

[PyMOL] Moving CGOs and getting matrix

Apparently, one can go into edit mode, and select a CGO and move and translate it. That's great, but I can't recover those transformations in a matrix, as I can with molecular objects (cmd.get_object_matrix). Any suggestions? _ Mark A. Saper, Ph.D

[PyMOL] Cf

Mark Saper sa...@umich.edu 734 276 6505 Mobile -- Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP

[PyMOL] D

Mark Saper sa...@umich.edu 734 276 6505 Mobile -- Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP

[PyMOL] Yt

Mark Saper sa...@umich.edu 734 276 6505 Mobile -- Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP

[PyMOL] Ray tracing problems

it? Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu phone (734) 764-3353 fax (734

[PyMOL] Access viewport size

sets the viewport. Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu phone (734) 764

[PyMOL] convert surface from pymol into a CCP4 map

as good as the one from PyMOL. Any other approaches to this? -Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109

[PyMOL] PDB changed CONNECT records

conformations are now interconnected when using the current 1ABE. The old 1ABE (from 1993) seems fine. Should setting connect_mode to 0 before loading PDB fix it? I don't think it does. Thanks, Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry

[PyMOL] Metadata for image

as usual. This idea could be expanded to save other things to the meta file (object information). -Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N

[PyMOL] Wizard modification

if it were in the wizard. Thanks, Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734

Re: [PyMOL] PyMOL-users Digest, Vol 3, Issue 18

I've tested two Kensington PilotMouse Laser Wireless mice and the middle button only works occassionally. I returned them for refund. I think the problem is what you said -- pressing activates the side- to-side scroll which overrides the middle click. I've also tried an MS Notebook Laser

[PyMOL] Kensington Laser Wireless Mouse

the manufacturer's software. -Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734

RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

and also adjust the shininess value. -Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax

[PyMOL] set_key

Why does this work: from pymol import cmd cmd.set_key ('CTRL-A', cmd.hide, ('sticks', 'joe_closed' ) ) and this doesn't? from pymol import cmd cmd.set_key ('CTRL-A', cmd.disable, ('joe_closed') ) _ Mark A. Saper, Ph.D. Associate

[PyMOL] Set all settings to default

_ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http

Re: [PyMOL] Set all settings to default

Warren, The problem is with ray tracing a surface from an old_session.pse. Much better results if you retrace it with the version that created it. Thanks for your help. Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics

[PyMOL] GUI

_ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http

[PyMOL] Lighting models b29 vs. b31

in beta31? Thanks, Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353

[PyMOL] MacPyMOL command entry

commands are. Many thanks, Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Associate Research Scientist in Biophysics Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 North University Ave Ann Arbor MI 48109

[PyMOL] OS X 10.4.3 comment

Quite a shock to read about the OS X 10.4.3 problem. I upgraded without a second thought and now I have the same problem on my 12 powerbook. This is with beta14 I believe. When I try the single window beta19 it seems to be less of a problem. -Mark _ Mark

[PyMOL] MacPyMOL 0.99b19

this? _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

RE: [PyMOL] edgelines between molecules

Balaji _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734

Re: [PyMOL] Need testers for new MacPyMOL on Tiger

to hide the top window with a key command? Also would it possible for it to reopen if someone dragged something onto the main window? If not, then I'll just get used to it. Thanks, Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry

[PyMOL] pymol -cp gives errors

cmd.do(l) File /opt/packages/pymol/modules/pymol/commanding.py, line 247, in do if _raising(r): raise pymol.CmdException CmdException: pymol.CmdException instance at 0xb7d3b4ac What am I doing wrong? The system has python 2.3.4 installed. Mark _ Mark

[PyMOL] PyMOL author??

Seems like Apple thinks that PyMOL was written by Michael Love!? Go to http://www.apple.com/science/software/lifescience.html towards end of page. _ Mark A. Saper, Ph.D. sa...@umich.edu (734) 764-3353 fax (734) 764-3323 http

[PyMOL] combine distance objects

How about disable _dist* enable _dist* Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa

[PyMOL] graphics boards

. Of the myriad of models available, could anyone help narrow the choices for me? Price range $150. Thanks, Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109