[PyMOL] Problem with ribbon

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

Re: [PyMOL] How to store matrix settings for individual scenes?

ot;\n") st = cmd.get_view(output=3) f.write(st) f.write("#Viewport when rendered:" + "\n") st=cmd.get_viewport(output=3) f.write(st) f.close() return r cmd.extend('png',mypng) __

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

ep_name, "?_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 t

[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 cl

[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. S

[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 ma

[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 ma

[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 ma

[PyMOL] Ray tracing problems

? 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] Rebuild

ow surface the surface swells slightly to account for the hydrogens. Is this a bug? or a feature? Also, is it appropriate to show surfaces in publication in the presence of the H's? Or does the 1.4 Å probe sphere that PyMOL uses intended to account for them? Mark _____

[PyMOL] convert surface from pymol into a CCP4 map

it doesn't look 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

[PyMOL] PDB changed CONNECT records

sugar 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

[PyMOL] Metadata for image

to also output all of the view matrix to a file that is saved with the .vew extension. The png file is saved 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

Re: [PyMOL] ribbon-like with one color

. _ 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] Wizard modification

r students 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) 764-3353

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

thout 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

[PyMOL] New MacBook

I'm very interested in knowing whether PyMOL is usable on the new MacBook considering that it has Intel integrated graphics. Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan

Re: [PyMOL] Producing publication quality images

You can easily change the resolution (dpi) of an image without changing the number of pixels, by editing the file in Photoshop (in Image Size, change resolution without rescaling) or in GraphicConverter (on Mac). _ Mark A. Saper, Ph.D. Associate Professor of

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) 764-3353

[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') ) _

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] 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

[PyMOL] GUI

endering options). 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] Lighting models b29 vs. b31

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] Re: macpymol update

t You can reach the person managing the list at pymol-users-ad...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. OS X 10.4.3 comment (Mark A Saper) 2. Re:

[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 _ M

[PyMOL] MacPyMOL 0.99b19

? _ 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

alaji _ 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

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 Chem

[PyMOL] pymol -cp gives errors

l/parser.py", line 88, in stdin_reader cmd.do(l) File "/opt/packages/pymol/modules/pymol/commanding.py", line 247, in do if _raising(r): raise pymol.CmdException CmdException: What am I doing wrong? The system has python 2.3.4 installed. Mark ____

[PyMOL] New transform_odb script

the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN. See http://www.pymolwiki.org/index.php/Transform_odb Mark _____ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Build

[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] view's in pymol and movie

mmand in PyMol to do this. 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

[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] MacPyMol beta 27

There are some weird things going on in MacPyMol 0.98beta 27. Are these known bugs? Wizard Sculpting from menu doesn't work. In mouse edit mode, control left button is behaving like control-shift left button. Suggestions? _ Mark A. Saper, Ph.

[PyMOL] animation ... fading objects in and out

objects in general? I tried using mvSet to ramp the "transparency" parameter applied to the specific object, but it didn't work. Suggestions? Thanks, Mark _________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Divisio

[PyMOL] graphics boards

f 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

[PyMOL] POVRAY and Smooth Triangles ?

I recall reading something about a patch that is necessary when running povray from pymol in order to implement the smooth_color_triangle setting. Could someone point me to this description? Thanks, Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological

[PyMOL] Depth-cueing/Fog in Ray Trace

ld I turn depth cue off? What's the diff between depth cue and fog? From my experiences depth-cueing should be a blending of model with background color. Suggestions? -Mark Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Associate Research Scientist,