[PyMOL] Ray tracing problems
When I ray trace a surface, the colors on the surface appear to have a smaller color depth. In other words, there are finite boundaries between different shades of colors rather than a smooth gradient. Could the problem be color-dependent? Has anyone seen this? Any ideas how to fix 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) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/ -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ 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
[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 market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ ___ 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
[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 market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ ___ 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
[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 market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ ___ 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
[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. Associate Professor of Biological Chemistry, University of Michigan -- Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk ___ 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
[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 class of "scene" settings which are treated in this manner. The current workaround is to create separate objects which are enabled/disabled differentially. This would be extremely useful, especially for making movies. Could priority for this be increased? Many thanks Mark -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk ___ 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
[PyMOL] 1.7.6.6 does not display a 1.7.4.4 .pse ifle.
I guess this is for Schrodinger representative.
I have a .PSE file (21.8 Mbyte) that does not open properly in 1.7.6.6. The
file has about 10 scenes in it.
Here are the errors:
Executive: Loading version 1.744 session...
Selector-Error: Invalid selection name "on".
?_scene_EcLpoA HTH1 on 4gpk HTH2 with 4gpk peptide_lines<--
Traceback (most recent call last):
File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/__init__.py",
line 262, in exec_deferred
cmd.load(a, quiet=0)
File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/importing.py",
line 912, in load
partial=partial,steal=1)
File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/importing.py",
line 96, in set_session
if not apply(a,(session,),{'_self':_self}): # don't stop on errors...try to
complete anyway
File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/viewing.py",
line 1296, in session_restore_scenes
_convert_legacy_scene(key, data, _self)
File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/viewing.py",
line 1341, in _convert_legacy_scene
_self.show(rep_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 to examine the file? If so contact me off list.
-Mark
_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Currently on sabbatical:
Laboratory of Susan Buchanan, Ph.D.
NIDDK, National Institutes of Health, Bethesda, MD 20892-8030
sa...@umich.edu mobile (734) 276-6505
--
___
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
Re: [PyMOL] How to store matrix settings for individual scenes?
I think this is related to the question about view setting. I rewrote the png
command (see below) to simultaneously output my image, but also output the
entire matrix and viewport with same name as the image but with filetype .vew.
That file can then be run with “@“ to recall the view. The output file also
contains the name of the .pse file. If one wants this per scene rather than
image, I assume one can rewrite the scene command too.
from pymol import cmd
import os
import re
import string
# import selector
def __init__(self):
cmd.extend('png',mypng)
def mypng(fname, quiet=1):
r = 1
format = 'vew'
cmd.png(fname, dpi=300, quiet=0)
sname = fname
if re.search("\.png$",fname):
fname = re.sub("\.png$","",fname)
fname = fname + ".vew"
fname = os.path.expanduser(fname)
fname = os.path.expandvars(fname)
f=open(fname,"w")
st=cmd.get("session_file")
f.write("#Session file: " + st + "\n")
f.write("#View matrix for " + sname + ".png" + "\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)
___
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III sa...@umich.edu +1 (734) 764-3353
On Mar 7, 2016, at 1:26 PM, pymol-users-requ...@lists.sourceforge.net wrote:
> Re: [PyMOL] How to store matrix settings for individual scenes?
--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval___
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
[PyMOL] pymol -cp gives errors
Hi, I have PyMOL version 0.99b14 installed on Linux . I am running it interactively without the GUI using the command pymol -cp . Whenever I accidentally type a return (null line) the PyMOL (or Python) interpreter crashes with this message: Traceback (most recent call last): File "/opt/packages/pymol/ext/lib/python2.3/threading.py", line 436, in __bootstrap self.run() File "/opt/packages/pymol/ext/lib/python2.3/threading.py", line 416, in run self.__target(*self.__args, **self.__kwargs) File "/opt/packages/pymol/modules/pymol/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 _____ 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
Re: [PyMOL] Need testers for new MacPyMOL on Tiger
Warren, Thanks for your hard work in preparing this version. It will be very convenient. My major use of the upper window is for convenience in dragging and dropping commands from other programs into MacPyMOL. Because of that I usually kept it behind the main window. Is it possible 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 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
RE: [PyMOL] edgelines between molecules
Balaji: I've done this by making a surface of just the domain I want to highlight, then bring it into Photoshop. Select the background, then invert the selection. Then convert selection to path and then stroke the path. Here is an example: [ Attachment only sent to Balaji, available on request ] Layer 0 is a regular surface of the residues involved in a dimer interface. Layer 1 is the stroked path. Layer 2 is a surface with charge potential of the entire region. Displaying Layer 1 and Layer 2 gives the desired figure. Have fun, Mark Date: Wed, 19 Oct 2005 15:44:35 -0400 From: Balaji Bhyravbhatla To: pymol-users@lists.sourceforge.net Subject: [PyMOL] edgelines between molecules Hello All, I have a large mega-dalton multi chain structure that I would like to make an overview (surface) figure. Instead of using many colors (13subunits) I would like to use one color and demarcate the subunits by some other means.One way would be to generate some sort of edge lines between the molecules. Is that possible, if so how? If anyone has any other suggestions please send them my way, it would be highly appreciated. Thanks 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) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] MacPyMOL 0.99b19
I started using the new MacPyMOL beta and have discovered that it does not support keyboard qualifiers to emulate a multibutton mouse. This was very useful on my Powerbook as I could do most operations without plugging in a 3-button mouse. Has anyone also noted 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
[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 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] Re: macpymol update
Warren et al. I checked, and my Powerbook G4 12" has nVIDIA GeForce4 MX, with 32 Mb memory. Always worked fine before. Realize that there are two different types of flicker. There is the usual mild flicker as one rotates a model (seems more than it used to be), and there is a more global flickering that is most noticeable in the menu area on the right of the screen. Still haven't seen the major flickering problem with b19. I will check b25. -Mark On Nov 4, 2005, at 7:27 AM, pymol-users-requ...@lists.sourceforge.net wrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net 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: Mac OS X 10.4.3 (Brian J Goodfellow) 3. Re: problem with CASTp plugin (Sebastien Moretti) 4. Re: PyMOL-users digest, Vol 1 #1049 - 6 msgs (Jesper Karlsen) 5. Re: macpymol beta 21 bug? (Martin Montgomery) 6. Re: Re: macpymol beta 21 bug? (khin...@cea.fr) 7. Re: Re: macpymol beta 21 bug? (Martin Montgomery) --__--__-- Message: 1 From: Mark A Saper Date: Thu, 3 Nov 2005 23:53:30 -0500 To: pymol-users@lists.sourceforge.net Subject: [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 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html --__--__-- Message: 2 Cc: pymol-users@lists.sourceforge.net From: Brian J Goodfellow Subject: Re: [PyMOL] Mac OS X 10.4.3 Date: Fri, 4 Nov 2005 09:00:07 + To: Warren DeLano Warren, with 0.99beta25 the problem still exists. After loading a molecule =20 there's no flickering but if I do a ray trace then the flickering =20 starts when I rotate. Shifting the window stops the flickering. By running show cartoon after loading I can also get the flickering. =20 Again, moving the window stops it. Brian On Nov 4, 2005, at 3:40 AM, Warren DeLano wrote: Brian, Can you confirm that this problem exists in the very latest beta? =20 I can't reproduce on my iMac G5 http://delsci.com/beta Is there any special trick to get it to happen? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-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 Brian J Goodfellow Sent: Thursday, November 03, 2005 2:17 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mac OS X 10.4.3 Hi Mac users, has anyone noticed an annoying flickering appearing when rotating a molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If the window is moved then the flickering disappears. However, if a ray trace is then drawn the problem starts again until the window is moved again - very annoying! Brian Goodfellow *** Brian J Goodfellow Departamento de Qu=CCmica Universidade de Aveiro 3810-193 Aveiro, Portugal Tel: +351 234 401506, Fax: +351 234 370084 http://www.dq.ua.pt/ingles/index_mem.htm *** --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --__--__-- Message: 3 Date: Fri, 04 Nov 2005 10:59:11 +0100 From: Sebastien Moretti To: jermainejenk...@netscape.net, pymol-users Subject: Re: [PyMOL] problem with CASTp plugin Hello,=20 We are running Python v2
[PyMOL] MacPyMOL command entry
Hi, Happy Holidays everyone. This is actually a bug report for Warren. If you have time, could you work on the implementation of the command recall option (up and down arrow) in the command text input field in the OS X-specific part of the window. It often forgets what the previous 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 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] Lighting models b29 vs. b31
I know that the lighting model for ray tracing in beta 31 is different than beta 29. But ray tracing of surfaces looks significantly better in beta 29. Beta 29 is brighter and the specular highlights are more subtle (less contrast). Any suggestions how to emulate beta29 appearance 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) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] GUI
Hi Warren, Why can't we have little check marks in the main menu that indicate the current setting? For example, Setting>Rendering>Antialias gets a check, but selecting Setting>Rendering>Shadows>None doesn't give a check (as do any of the other rendering 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) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] Set all settings to default
0.99 and 0.98 have different ray tracing and lighting models. When I read an old .pse file into .99, are the settings in the old file converted to the new style? Is there a way to reset all of the settings to default values, without modifying the objects themselves? 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) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
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 Research Division, University of Michigan
On Feb 28, 2006, at 6:13 PM, Warren DeLano wrote:
Hi Mark,
Hmm. PyMOL attempts to migrate old settings into the new model,
but it
isn't perfect and one may need to fiddle with the various settings
after
migration. We'll need a new feature to reinitialize settings without
deleting content so thanks for the suggestion! In the meantime,
you can
do something like this:
from chempy import io
sess=io.pkl.fromFile("old_session.pse")
del sess['settings']
io.pkl.toFile(sess,"new_session.pse")
load new_session.pse
which will load the old session with new default settings.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-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
Mark A Saper
Sent: Tuesday, February 28, 2006 11:12 AM
To: Pymol
Subject: [PyMOL] Set all settings to default
0.99 and 0.98 have different ray tracing and lighting models.
When I read an old .pse file into .99, are the settings in
the old file converted to the new style? Is there a way to
reset all of the settings to default values, without
modifying the objects themselves?
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) 764-3353fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
---
This SF.Net email is sponsored by xPML, a groundbreaking
scripting language that extends applications into web and
mobile media. Attend the live webcast and join the prime
developer group breaking into this new coding territory!
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&;
dat=121642
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
[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 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
RE: [PyMOL] Displaying/defining double bonds in a ligand molecule
Wulf et al, I've had similar results to what you report even with a session file created with the latest version of PyMol. You should first try what Warren suggests. Then, if the specular highlights still look too contrasty, you can try reducing the specular_intensity to about 0.2 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 (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
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 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) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[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 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] Kensington Laser Wireless Mouse
Has anyone successfully used this relatively new mouse with MacPyMol. The middle button is a bit screwed up. Sometimes when I click it, it seems to activate the scroll, and widens the slab. But then the scroll wheel doesn't work. Something very strange. This happens with or without 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) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html Biophysics Interdepartmental Graduate Program: http://www.umich.edu/ ~biophys
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 Mouse and the button didn't work either. I know that many other mice work --- probably the ones without the horizontal scroll. -Mark On Aug 22, 2006, at 5:07 PM, pymol-users- requ...@lists.sourceforge.net wrote: From: Ramachandran Murali Date: August 21, 2006 8:43:00 PM GMT-04:00 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] kensington three button mouse in mac book pro-issue Hi, I am using Kensington three-button mouse on a Mac book pro (17") laptop. In pymol, when i press the middle button (for translation), it switches to horizontal scroll. The translation function is not working! Has anyone experienced similar problem?. Any fix or work around? Thanks Murali
[PyMOL] Wizard modification
Is there a way to modify the code of the Measurement wizard or to load a new copy of it? I'd like a Nonpolar neighbor option that will look for nonpolar atoms with > 3.0 and <4.1 Å from picked atom. I've written an alternative command to do this but it would be useful for 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) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
Re: [PyMOL] ribbon-like with one color
There are actually other spectrums built into the PyMOL. To use one of them, type spectrum palette=, selection= The list of built-in palettes are in cmd.py of the code. All seem to be multi color; so there are none that are just different shades of 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html Biophysics Interdepartmental Graduate Program: http://www.umich.edu/ ~biophys
[PyMOL] Metadata for image
Hi Gilleain and Andreas,
This is what I use to save information about the image. I redefine
the png command.
from pymol import cmd
import os
import re
import string
import selector
def __init__(self):
cmd.extend('png',mypng)
def mypng(fname, quiet=1):
r = 1
format = 'vew'
cmd.png(fname, quiet)
if re.search("\.png$",fname):
fname = re.sub("\.png$","",fname)
fname = fname + ".vew"
fname = os.path.expanduser(fname)
fname = os.path.expandvars(fname)
f=open(fname,"w")
f.write("#View matrix for " + fname + "\n")
st = cmd.get_view(output=3)
f.write(st)
f.close()
return r
cmd.extend('png',mypng)
This command will use the name that you specify for the png file 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 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
Biophysics Interdepartmental Graduate Program: http://www.umich.edu/
~biophys
[PyMOL] PDB changed CONNECT records
This was previously discussed in an archived email but I can't find it right now. Does the setting connect_mode=0 use the CONECT records in the PDB file or not? I think it does. Apparently in pdb code 1ABE, the CONECT records were changed in a 2005 revision. Two alternate 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 Chemistry Biophysics, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] convert surface from pymol into a CCP4 map
I have a nice cavity surface that I've made in PyMOL. I'd like to convert it to some type of envelope in CCP4 map format, for input into Coot. I know that surfaces can be saved in .wrl format. I've also tried using Voidoo to prepare a pseudo-map representing the cavity, but 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 Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/ -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ 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
[PyMOL] Rebuild
If a model is modified, the "rebuild" command does not always update the surface. For example, show lines, theProtein and not elem H show surface show lines, elem H rebuild The surface does not change. But if I now, hide surface show 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 _________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan sa...@umich.edu phone (734) 764-3353 fax (734) 764-3323 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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
[PyMOL] Access viewport size
The output of the get_view command does not save the size of the viewport. Thus if you want to recreate an image for ray tracing so it will have the same size and scale, one also needs to save the viewport dimensions. Is there some way to access this information? The viewport command only 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) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/ -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ 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
[PyMOL] Depth-cueing/Fog in Ray Trace
Hi, I've rendered a cartoon model with these parameters: PyMOL>set fog,0.8 PyMOL>set antialias = 1 PyMOL>bg_color white PyMOL>set ray_trace_fog=1 PyMOL>set spec_power=200 PyMOL>set spec_refl=1.5 Rather than fading to white, the model fades to grey in the distance. Should 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, Biophysics Research Division Biophysics Research Division sa...@umich.edu University of Michigan Phone: (734) 764-3353 930 North University Ave FAX: (734) 764-3323 Ann Arbor, MI 48109-1055 U.S.A.
[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 Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 sa...@umich.edu (734) 764-3353 fax (734) 764-3323
[PyMOL] graphics boards
I know this has been discussed before on this list. I need a graphics board for a Linux RH 9.0 running on Dell Optiplex GX270. The applications will be O and Pymol and similar programs. Stereo-capable would be preferred. I've been told that NVidia is more compatible with Linux. 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 48109-1055 sa...@umich.edu (734) 764-3353 fax (734) 764-3323 http://www-personal.umich.edu/~saper
[PyMOL] animation ... fading objects in and out
I'm using MasterMovie.py (the enhanced rTools movie module). I've made two objects, one is a cartoon representation of a structure, the other is CPK. During my animation I want to start with the cartoon, then cross-fade into the CPK. What paremeters control the transparency of 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 Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 sa...@umich.edu (734) 764-3353 fax (734) 764-3323 http://www-personal.umich.edu/~saper
[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.D. sa...@umich.edu (734) 764-3353 fax (734) 764-3323
[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...@umich.edu (734) 764-3353 fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
On Mar 8, 2005, at 11:27 PM, pymol-users-requ...@lists.sourceforge.net
wrote:
Send PyMOL-users mailing list submissions to
pymol-users@lists.sourceforge.net
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/pymol-users
or, via email, send a message with subject or body 'help' to
pymol-users-requ...@lists.sourceforge.net
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. Re: combine distance objects (Robert Campbell)
2. [Re: [PyMOL] combine distance objects] (Viktor Hornak)
3. Re: combine distance objects (Michael George Lerner)
4. RE: combine distance objects (Garcia, Tzintzuni I.)
--__--__--
Message: 1
Date: Tue, 8 Mar 2005 10:55:20 -0500
From: Robert Campbell
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] combine distance objects
Hi,
Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote:
I want to create a lot of distance objects (in the hundreds)
between particular atomic pairs. Obviously I can make a
script like the following, inserting the exact atomic
selections that I want:
distance distobj12 = (atom1), (atom2)
distance distobj34 = (atom3), (atom4)
... etc.
However, I will end up with hundreds of distance object
controls on the right side of the pymol viewer. I want to
have just a SINGLE distance object that contains all of the
individual distance objects combined.
That way I could enable/disable the entire object with a
single click, or change the color, etc. Hundreds of
individual objects would be unmanageable.
Is there a way to do this? Thanks,
* Warren L. DeLano [2005-03-07 13:46]
wrote:
This is a reasonable request, but no, it isn't possible right now --
sorry.
If it isn't necessary to be able to turn the distances on and off,
then you
can name them using a preceeding underscore "_" so that they are
omitted
from the object list.
But in fact one *can* still turn them on and off, with the "enable" or
"disable" command on the command line:
enable _dist1
disable _dist1
And it would be straightforward to put those commands within a loop:
# turn them all off:
for i in range(100):
cmd.disable("_dist1%s" % i)
# turn them all on:
for i in range(100):
cmd.enable("_dist1%s" % i)
Change "100" to whatever is appropriate.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associatephone:
613-533-6821
Dept. of Biochemistry, Queen's University, fax:
613-533-2497
Kingston, ON K7L 3N6 Canada
http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
--__--__--
Message: 2
Date: Tue, 08 Mar 2005 11:31:16 -0500
From: Viktor Hornak
To: pymol-users@lists.sourceforge.net
Subject: [Re: [PyMOL] combine distance objects]
Robert Campbell wrote:
Hi,
Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote:
I want to create a lot of distance objects (in the hundreds)
between particular atomic pairs. Obviously I can make a
script like the following, inserting the exact atomic
selections that I want:
distance distobj12 = (atom1), (atom2)
distance distobj34 = (atom3), (atom4)
... etc.
However, I will end up with hundreds of distance object
controls on the right side of the pymol viewer. I want to
have just a SINGLE distance object that contains all of the
individual distance objects combined.
That way I could enable/disable the entire object with a
single click, or change the color, etc. Hundreds of
individual objects would be unmanageable.
Is there a way to do this? Thanks,
* Warren L. DeLano [2005-03-07 13:46]
wrote:
This is a reasonable request, but no, it isn't possible right now --
sorry.
If it isn't necessary to be able to turn the distances on and off,
then you
can name them using a preceeding underscore "_" so that they are
omitted
from the object list.
But in fact one *can* still turn them on and off, with the "enable" or
"disable" command on the command line:
enable _dist1
disable _dist1
And it would be straightforward to put those commands within a loop:
# turn them all off:
for i in range(100):
cmd.disable("_dist1%s" %
[PyMOL] view's in pymol and movie
Mike, The routines that Scott cites were nicely incorporated into MasterMovie.py by Seth Harris (shar...@msg.ucsf.edu) that is derived from Kristian Rother's rTools (www.rubor.de) and modified . Email Seth to see where he hides the program. Warren ... Glad to hear there is a new command 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) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] New transform_odb script
The "transform_odb" script transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a file containing an "O"-style tranformation matrix (.odb) written by "O" or by any of 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 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://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] Problem with ribbon
Hi All & Thomas There appears to be a problem with ribbon representations. I am testing MacPyMOL on v 1.8.1.1 but the same behavior is seen with 1.8.0.4. Create a ribbon of a test protein, for example, show ribbon, test and (resi 10:20 or resi 25:35) Double click 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 III sa...@umich.edu +1 (734) 764-3353 -- ___ 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
