Recent changes to support-requests

#76 Does a poor alignment in cealign negate a good alignment in super?

Thomas Holder — Fri, 09 Mar 2018 06:38:20 -0000

Ticket moved from /p/pymol/bugs/198/

#73 Error when trying to download MacPyMOL version 0.99

Thomas Holder — Thu, 01 Aug 2013 08:27:05 -0000

status: open --> closed
Group: -->

Some qustions about selection

own — Wed, 28 Sep 2011 07:48:41 -0000

Hello I\'m new user of PyMol. I\'ve already learned some basc functions of PyMol but I couldnt find in the existing tutorials some intresting for me features 1\) I wounder to know if there is possible way of selection some SS elements \( e.g specific helix\) from my protein with the exception of common way of selection of some RESNUMS or atoms. 2\) How I can obtain psi\\\phy angles map for my protein \( E.g I want to select some regment of my protein and obtained above values for the atoms in this segment ? 3\) Could you provide me with the better tutorial that I\'ve alredy found \( vey old versions dated by 2003-2004\) Thank you Own

Cz2LxY vjuzjynxykhj,

Anonymous — Fri, 12 Feb 2010 15:59:55 -0000

Cz2LxY <a href="http://vjuzjynxykhj.com/">vjuzjynxykhj</a>, \[url=http://qajhgjvxfwdj.com/\]qajhgjvxfwdj\[/url\], \[link=http://kvarxpsanafl.com/\]kvarxpsanafl\[/link\], http://actfgcftzktp.com/

Error when trying to download MacPyMOL version 0.99

Anonymous — Thu, 21 Jan 2010 21:40:29 -0000

Hello, I received the following error when trying to download the 0.99 version of MacPyMOL: Page Not Found We cannot locate the page you're looking for. Please check the address and make sure all letters are lowercased with no spaces. You may also move to a different page by using the links in the menu bar above. Any help as to how I can download the 0.99 version would be greatly appreciated. Thank you\!

Error when trying to download MacPyMOL version 0.99

Anonymous — Thu, 21 Jan 2010 21:40:29 -0000

Ticket 73 has been modified: Error when trying to download MacPyMOL version 0.99
Edited By: Thomas Holder (speleo3)
Status updated: u'open' => u'closed'

Help with color_b

Anonymous — Sat, 16 Jan 2010 03:20:17 -0000

I kept getting the error message of Color error: Unknown color at the last step of trying to color the protein with an rgb gradient according to B factors. I loaded the data2bfactor.py and color\_b.py files, run data2b\_res command with proper labeling of B values at each protein residue correctly shown. When I run the last line, color\_b\('all', nbins=6, gradient='rgb'\), the bins were even categorized to proper B ranges, and then I got the Unknown color error. Could someone pass a clue? Thanks a lot\!

Pymol fails to render molecules when run as thread

Anonymous — Wed, 06 Jan 2010 15:12:42 -0000

Hi, I have written small application to fetch molecules stored in database and display selected with pymol. Unfortunately issuing command pymol.cmd.read\_sdfstr\(\) or pymol.cmd.load\(\) results in "broken" molecules - just as it is on attached image. At the same time I loose ability to pick molecules via open/save dialogs, only keyboard works My code to run pymol as thread is: def run\(\): \_\_main\_\_.pymol\_launch = 0 if hasattr\(\_\_main\_\_,"pymol\_argv"\): pymol\_argv = \_\_main\_\_.pymol\_argv else: pymol\_argv = sys.argv modules\_path = os.environ\['PYMOL\_PATH'\]+'/modules' if modules\_path not in sys.path: sys.path.append\(modules\_path\) import pymol pymol.invocation.parse\_args\(pymol\_argv\) pymol.start\_pymol\(\) \#----------------------------------------------\# t = threading.Thread\(target=run\) t.setDaemon\(1\) t.start\(\) Thank you in advance for any help

how to clip/slab selected objects only

Anonymous — Wed, 25 Nov 2009 20:23:31 -0000

I am trying to display a ligand \(as sticks and balls\) binding to a protein surface pocket \(surface representation of protein\). To make it look nice, I'd need to clip \(or slab\) the protein, but not the ligand. Is there a way of excluding objects from clipping? Thanks for reading this.

TclError from PyMol on Centos5.4

Anonymous — Thu, 05 Nov 2009 00:29:08 -0000

I've installed PyMol on Centos5.4 and receive the error message below when executing the application. This happens with versions 1.1r1 and 1.2r2. I have verified that Tcl/TK are installed. This Executable Build integrates and extends Open-Source PyMOL 1.1r1. OpenGL graphics engine: GL\_VENDOR: NVIDIA Corporation GL\_RENDERER: Quadro FX 3400/PCI/SSE2 GL\_VERSION: 2.1.0 NVIDIA 96.31 Hardware stereo capability detected. Adapting to Quadro hardware. Detected 2 CPU cores. Enabled multithreaded rendering. Traceback \(most recent call last\): File "/home/kdelisle/software/PyMol\_1\_1r1/modules/pmg\_tk/\_\_init\_\_.py", line 35, in run PMGApp\(pymol\_instance,skin\).run\(poll\) File "/home/kdelisle/software/PyMol\_1\_1r1/modules/pmg\_tk/PMGApp.py", line 347, in \_\_init\_\_ self.runSkin\(\) File "/home/kdelisle/software/PyMol\_1\_1r1/modules/pmg\_tk/PMGApp.py", line 276, in runSkin self.skin.setup\(\) File "/home/kdelisle/software/PyMol\_1\_1r1/modules/pmg\_tk/skins/normal/\_\_init\_\_.py", line 2793, in setup self.createInterface\(\) File "/home/kdelisle/software/PyMol\_1\_1r1/modules/pmg\_tk/skins/normal/\_\_init\_\_.py", line 2766, in createInterface self.balloon = Pmw.Balloon\(self.root\) File "/home/kdelisle/software/PyMol\_1\_1r1/ext/lib/python2.4/site-packages/Pmw/Pmw\_1\_2/lib/PmwBalloon.py", line 27, in \_\_init\_\_ Pmw.MegaToplevel.\_\_init\_\_\(self, parent\) File "/home/kdelisle/software/PyMol\_1\_1r1/ext/lib/python2.4/site-packages/Pmw/Pmw\_1\_2/lib/PmwBase.py", line 974, in \_\_init\_\_ MegaArchetype.\_\_init\_\_\(self, parent, Tkinter.Toplevel\) File "/home/kdelisle/software/PyMol\_1\_1r1/ext/lib/python2.4/site-packages/Pmw/Pmw\_1\_2/lib/PmwBase.py", line 352, in \_\_init\_\_ hullClass, \(parent,\)\) File "/home/kdelisle/software/PyMol\_1\_1r1/ext/lib/python2.4/site-packages/Pmw/Pmw\_1\_2/lib/PmwBase.py", line 524, in createcomponent widget = apply\(widgetClass, widgetArgs, kw\) File "/home/kdelisle/software/PyMol\_1\_1r1/ext/lib/python2.4/lib-tk/Tkinter.py", line 1906, in \_\_init\_\_ BaseWidget.\_\_init\_\_\(self, master, 'toplevel', cnf, \{\}, extra\) File "/home/kdelisle/software/PyMol\_1\_1r1/ext/lib/python2.4/lib-tk/Tkinter.py", line 1862, in \_\_init\_\_ self.tk.call\( TclError: unknown color name "black"