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 (http

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 j

Re: [PyMOL] Open Source PyMOL v1.5.0.1

On 2/13/2012 11:27 AM, Jason Vertrees wrote: > Greetings, > > It is my pleasure to announce the release of open source PyMOL > v1.5.0.1. The source code has been committed to the open-source > repository. It is revision 3976. An svn tag and downloadable bz2 > source file were also created. All of

Re: [PyMOL] Open Source PyMOL v1.5.0.1

equisite files now. > > Cheers, > > -- Jason > > On Mon, Feb 13, 2012 at 3:47 PM, Christoph Gohlke wrote: >> >> >> On 2/13/2012 11:27 AM, Jason Vertrees wrote: >>> Greetings, >>> >>> It is my pleasure to announce the release of open sou

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 on-screen

Re: [PyMOL] plugin errors in pymol 1.7.2.1

Try the 64 bit version of OpenBabel at 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

Hi 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,

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

[PyMOL] PyMOL 1.2r0 for Windows

Hello, in case anyone wants to try PyMOL 1.2r0 on Windows, I have compiled 32-bit binaries that should work with a standard installation of Python 2.6.2 (www.python.org). The build is completely unsupported and available on my homepage. http://www.lfd.uci.edu/~gohlke/#pythonlibs Regards, Chr

[PyMOL] PyMOL/CEAlign for Windows

on.org) 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 -- Ret

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 t

Re: [PyMOL] PyMOL/CEAlign for Windows

selected program to open this kind of file" > > The Windows OS 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

Re: [PyMOL] Pymol binaries for Windows

Unofficial binaries are at . Christoph On 1/30/2010 12:24 PM, Nikola Wenta wrote: > Hello all! > I became aware that Pymol, a nice x-ray structure viewer, is no longer > available as binary but rather needs to be compiled from source code. > Whil

Re: [PyMOL] Pymol binaries for Windows

To quote Warren L. DeLano on building PyMOL on Windows: "Given enough effort, native compilation is certainly do-able, but it is not intended to be easy... nor commonplace." See and

Re: [PyMOL] Compilation issues on Win32 vs2008

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

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 t

Re: [PyMOL] Update & Submitting Bugs

t;PyMOL Bug" in the title). 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 1

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

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 vers

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 > > I get

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 Pyt

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 wr

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 extensio

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

s * G) 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, 2

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 2.

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 mou