[PyMOL] PyMOL/CEAlign for Windows

) and numpy (http://www.scipy.org). Note that these binaries are unofficial and unsupported. Best, Christoph Gohlke Laboratory for Fluorescence Dynamics University of California, Irvine http://www.lfd.uci.edu -- Return

Re: [PyMOL] PyMOL/CEAlign for Windows

On 12/11/2009 2:40 AM, MyLinkka wrote: Thanks! It works nicely here! One thing I want to ask is Is there a way to make file association? e.g. associate *.pdb with pymol. Ting To associate PyMOL with PDB files, adjust the Python and PyMOL paths in the attached PDB_file.reg registry file and

Re: [PyMOL] PyMOL/CEAlign for Windows

will then modify the registry to associate *.pdb files with PyMOL. Good luck! -Tom -Original Message- From: Christoph Gohlke [mailto:cgoh...@uci.edu] Sent: Friday, December 11, 2009 9:57 AM To: mylin...@gmail.com; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL

Re: [PyMOL] Compilation issues on Win32 vs2008

Take a look at the patch at http://sourceforge.net/tracker/?func=detailaid=2819455group_id=4546atid=104546, especially the last part. Another recommendation: Use freeglut 2.6.0 rc1, not glut. Christoph Gohlke Laboratory for Fluorescence Dynamics University of California, Irvine http

Re: [PyMOL] Update Submitting Bugs

What is the URL of the Schrodinger bug tracker? The PyMOL SourceForge tracker is disabled. Thanks, Christoph On 2/17/2010 11:35 AM, Jason Vertrees wrote: PyMOLers, * In order to keep all bugs in one place please email your bugs to h...@schrodinger.com instead of using the SourceForge

Re: [PyMOL] Update Submitting Bugs

). They are immediately filed and assigned to me. I chose to turn off the SourceForge tracker because I do not want to miss bugs or spend my time duplicating tracking efforts, as I was. Thanks, -- Jason On Thu, Feb 18, 2010 at 12:15 AM, Christoph Gohlke cgoh...@uci.edu wrote: What is the URL

Re: [PyMOL] Rotation/Translation

On 5/29/2010 8:21 AM, J. Fleming wrote: Hello, I've been using 'super' to align the C-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and

Re: [PyMOL] unable to open the file

You can try the attached patch. It fixes three issues: * is_string() returns False in case of unicode filenames * Python/Tk bug http://bugs.python.org/issue5712 * filenames containing whitespace Christoph On 1/23/2011 7:02 AM, wang_qi wrote: Hello, everyone, I have downloaded the pymol of

Re: [PyMOL] PyMOL Project Updates Open Source PyMOL v1.4b1

On 4/1/2011 2:34 PM, Jason Vertrees wrote: Greetings PyMOLers, I got back from my trip last night and immediately started putting the new features into the open source branch as promised. I've finished the merge, pushed the changes to SourceForge (revision 3938), and uploaded a tar file

Re: [PyMOL] global illumination, volume representation and ipython

On 4/11/2011 10:05 AM, Jason Vertrees wrote: Hi Marius, Also right clicking on the volume representation raises the following error Error: 2 ... The right-click on background exception has been fixed. The code, a few other fixes, and a new feature for testing :-), has just been pushed

Re: [PyMOL] Open Source PyMOL v1.5.0.1

Hi Jason, Thank you. Works well now. The speed improvements are very significant (Win64, GeForce GTX 560). Btw, the splash screens are still at version 1.3.x. Christoph On 2/13/2012 12:50 PM, Jason Vertrees wrote: Hi Christoph, I just noticed that myself. I'll add the requisite files now.

Re: [PyMOL] PyMOL 1.6 pre-release announcement

On 3/24/2013 3:02 AM, Thomas Holder wrote: Dear PyMOL users, The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all

Re: [PyMOL] plugin errors in pymol 1.7.2.1

Try the 64 bit version of OpenBabel at http://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel Christoph On 12/20/2014 1:12 PM, Osvaldo Martin wrote: Hi Hena, Regarding Optimize plugin. You need to install OpenBabel and OpenBabel Python bindings (see instructions here

Re: [PyMOL] plugin errors in pymol 1.7.2.1

Christoph, I do not use Windows. I would be very thankful if you could check that the optimize-plugin works with the 64 bit version of OpenBabel that you mention. Could you please confirm that? Thanks in advance. Osvaldo. On Sat, Dec 20, 2014 at 8:14 PM, Christoph Gohlke cgoh...@uci.edu

Re: [PyMOL] PyMOL installation on Windows 7

Looks like pip is not installed correctly or your PYTHONPATH wrong (unset it). To install pymol from wheels for Python 2.7 64 bit installed at C:\Python27, download the following files: pip-6.0.8-py2.py3-none-any.whl numpy-1.9.2+mkl-cp27-none-win_amd64.whl Pmw-2.0.0-py2-none-any.whl

Re: [PyMOL] Problem with pymol installation

mol_launcher > 1.0 whl files, all of them downloaded from the Christoph Gohlke > webpage. However, after typing in the command prompt > > C:\Python27\python.exe pip-8.0.3-py2.py3-none-any.whl/pip install > --no-index --find-links="%CD%" pymol_launcher > >

Re: [PyMOL] Unofficial Windows PyMOL Binaries fails to run

On 2/13/2017 4:42 PM, Ioannis Michalopoulos wrote: > Dear all, > > I use Windows 10 64-bit with CUDA NVIDIA. I downloaded the Unofficial > Windows Binaries for PyMOL and its dependencies, for Python36, Python35 > and Python27, from: > > http://www.lfd.uci.edu/~gohlke/pythonlibs/ > > I installed

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

Hello, try to uninstall Pmw and reinstall it using Pmw-2.0.1-py3-none-any.whl from . C:\Python36\python.exe -m pip uninstall Pmw C:\Python36\python.exe -m pip install Pmw-2.0.1-py3-none-any.whl Christoph On 8/21/2017 8:27 AM, Vijay Masand

Re: [PyMOL] Windows PDB file for debugging pymol C extension?

I put a VS2015 build of svn rev 4189 including debug information files for the pymol source at Hope this helps. Christoph On 5/9/2018 7:34 AM, Gary Oberbrunner wrote: Hi; I'm running into a crash in Windows pymol, in the C

Re: [PyMOL] Windows PDB file for debugging pymol C extension?

) Line 2808C++ _cmd.cp36-win_amd64.pyd!OrthoAddOutput(_PyMOLGlobals * G, const char * str) Line 1175C++ _cmd.cp36-win_amd64.pyd!PCatchWrite(_object * self, _object * args) Line 2738C++ But that doesn't really tell me anything about where the actual heap corruption happened. On Wed, May 9, 2018 at 1:

Re: [PyMOL] Problem In using Pymol 2.4 through IDLE -Python 3

Try installing the Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019 Christoph On 10/23/2020 8:11 PM, Dr. Vijay Masand wrote: Hello PyMOL users I installed open source PyMOL

Re: [PyMOL] Scroll wheel not slabbing

Regarding Pmw: pip uninstall Pmw and install Pmw-2.0.1-py3-none-any.whl from Christoph On 5/2/2021 11:43 AM, Marko Hyvonen wrote: Hello PyMOLers Just installed open source 2.4 with Python 3.9 and all seems ok apart from the