[PyMOL] PyMOL/CEAlign for Windows

2009-12-10 Thread Christoph Gohlke 
Dear PyMOL for Windows users,

I have updated Windows binaries of PyMOL 1.2r3pre and CEAlign 0.9 for 
Python 2.4, 2.5, and 2.6 (32 and 64-bit) for download at 
http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol. They should work 
with a standard installation of Python 2.x (http://www.python.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

--
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
___
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] PyMOL/CEAlign for Windows

2009-12-11 Thread Christoph Gohlke 


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 then merge it to the Windows 
registry.


Christoph

REGEDIT4

[-HKEY_CLASSES_ROOT\.pdb]

[HKEY_CLASSES_ROOT\.pdb]
@=PDB.File
Content Type=chemical/x-pdb

[-HKEY_CLASSES_ROOT\PDB.File]

[HKEY_CLASSES_ROOT\PDB.File]
@=PDB File

[HKEY_CLASSES_ROOT\PDB.File\DefaultIcon]
@=C:\\PyMOL-1.2\\PyMOL.ico

[HKEY_CLASSES_ROOT\PDB.File\Shell]
@=

[HKEY_CLASSES_ROOT\PDB.File\Shell\open]

[HKEY_CLASSES_ROOT\PDB.File\Shell\open\command]
@=\C:\\Python26\\pythonw.exe\ -B -O \C:\\PyMOL-1.2\\pymol-launch.py\ %* 
\%1\
--
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
___
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] PyMOL/CEAlign for Windows

2009-12-11 Thread Christoph Gohlke 
That will work for the official PyMOL distribution only. PymolWin is not 
in the public SVN repository and the registry file is easier to use in 
computer lab environments.

Christoph

On 12/11/2009 12:38 PM, Thomas Stout wrote:

 A perhaps easier way is to right-click on a pdb file with the mouse and
 choose Open with... In that sub-menu select Choose program.  In the
 subsequent window that appears, select PymolWin as the program you want
 to open the PDB file with AND then also check the box underneath that
 says Always use the 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, 2009 9:57 AM
 To: mylin...@gmail.com; pymol-users@lists.sourceforge.net
 Subject: 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 then merge it to the Windows
 registry.


--
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
___
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] Compilation issues on Win32 vs2008

2010-02-15 Thread Christoph Gohlke 
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://www.lfd.uci.edu/~gohlke/


On 2/15/2010 1:17 PM, aaron bryden wrote:
 We are attempting to compile pymol on windows so that it is compiled
 against the version of python that we use in all of our other software
 (due to our IT situation this would make our plugin development
 substantially easier). Our version of python is 2.6. We are using the
 distutils method where our command to compile is 'python.exe setup.py build'
 After dealing with all of the dependencies and fixing os_predef.h to ask
 the linker to use recent versions of libraries it almost completely
 compiled. We are stuck at the end with the following link error:
  
 mfcs90.lib(nolib.obj) : error LNK2001: unresolved external symbol int
 __cdecl _
 AfxInitManaged(void) (?_AfxInitManaged@@YAHXZ)
 mfcs90.lib(stdafx.obj) : error LNK2001: unresolved external symbol int
 __cdecl
 _AfxInitManaged(void) (?_AfxInitManaged@@YAHXZ)
 
  We have looked for a way to get this symbol in our program and are at a
 loss. Google points to precompiled header issues but as far as we can
 tell, distutils is not making use of precompiled headers.
  
 If anyone has had any experience with this or any suggestions it would
 be greatly appreciated.
  
 thanks,
  
 aaron bryden
 
 
 
 --
 SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
 Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
 http://p.sf.net/sfu/solaris-dev2dev
 
 
 
 ___
 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

--
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
___
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] Update Submitting Bugs

2010-02-17 Thread Christoph Gohlke 
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 tracker.
 Schrodinger has a very nice bug tracker that we use; and, in the end
 it's just better to not duplicate effort.
 
 * I started pushing small changes into the open-source code and more
 are coming.  Please file bugs to the aforementioned address.
 
 * CEAlign is working on all my versions of PyMOL, so I'll be pushing
 that to the open-source soon.
 
 * We now have another server for FreeMOL (which maps right back to
 http://freemol.org/) and we also have control over the FreeMOL
 project.  When I get back to my office (where the files live) I'll
 update FreeMOL.
 
 Thanks,
 
 -- Jason
 

--
Download Intelreg; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs 
proactively, and fine-tune applications for parallel performance. 
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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] Update Submitting Bugs

2010-02-17 Thread Christoph Gohlke 
Good. Thanks for keeping PyMOL development going.

Christoph

On 2/17/2010 9:30 PM, Jason Vertrees wrote:
 Christoph,
 
 Schrodinger's tracker is internal only.  To submit a bug, just email
 your bugs to h...@schrodinger.com (for faster turnaround put something
 like 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 18, 2010 at 12:15 AM, Christoph Gohlke cgoh...@uci.edu wrote:
 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 tracker.
 Schrodinger has a very nice bug tracker that we use; and, in the end
 it's just better to not duplicate effort.

 * I started pushing small changes into the open-source code and more
 are coming.  Please file bugs to the aforementioned address.

 * CEAlign is working on all my versions of PyMOL, so I'll be pushing
 that to the open-source soon.

 * We now have another server for FreeMOL (which maps right back to
 http://freemol.org/) and we also have control over the FreeMOL
 project.  When I get back to my office (where the files live) I'll
 update FreeMOL.

 Thanks,

 -- Jason

--
Download Intelreg; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs 
proactively, and fine-tune applications for parallel performance. 
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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] Rotation/Translation

2010-05-30 Thread Christoph Gohlke 


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 name ca)

 What I would like to do is determine the rotation and translation of
 model B's second domain as it moves away from A's second domain.

 I can output a matrix after running super using:

 print cmd.get_object_matrix(A)

 How do I go from the matrix to an angle and distance?

 Thanks for any thoughts,
 Jon



To extract Euler rotation angles from the superimposition matrix you can 
use the euler_from_matrix function of the transformations.py module at 
http://www.lfd.uci.edu/~gohlke/code/transformations.py.html. If you 
rather have a rotation angle and axis use the rotation_from_matrix 
function. You might have to use the transpose of the matrix returned by 
PyMOL, not sure. The extraction of the translation vector has already 
been explained.

To find how domain #2 is translated and rotated in molecule B relative 
to A when the domains #1 of A and B are superimposed, you can write a 
Python script outside of PyMOL. The following untested (!) script 
assumes that you have (1) the C-alpha coordinates of molecule A and B as 
homogeneous coordinate numpy arrays of shape (4, *), and (2) the C-alpha 
atom indices that belong to domain 1 and 2 as Python sequences or slices:


import numpy
import transformations

# transform B such that domain1 of A and B overlap
S0 = transformations.superimposition_matrix(
  B[:, domain1], A[:, domain1])
B = numpy.dot(S0, B)

# calculate matrix to transform domain2 of A to B
S1 = transformations.superimposition_matrix(
  A[:, domain2], B[:, domain2])

# extract translation vector and Euler rotation angles from S1
translation = S1[:3, 3].copy()
eulerangles = transformations.euler_from_matrix(S1)


--
Christoph

--

___
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] unable to open the file

2011-01-23 Thread Christoph Gohlke 

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 version 1.3. and installed it on windows
XP successfully. But when selecting file-open to load my file, it
doesn't work and displays that the file is unable to be opend. Dose
anyone meet this problem? Ana how how can i solve it?
Thanks.
Qi Wang
2011-01-23
wang_qi





Index: pymol/modules/pymol/commanding.py
===
--- pymol/modules/pymol/commanding.py   (revision 3896)
+++ pymol/modules/pymol/commanding.py   (working copy)
@@ -89,7 +89,8 @@
 
 '''
 pymol=_self._pymol
-if not is_string(filename): # we're logging to Queue, not a file.
+# CG: is_string returns False in case of unicode filenames
+if not isinstance(filename, basestring): # we're logging to Queue, not 
a file.
 pymol._log_file = QueueFile(filename)
 _self.set(logging,1,quiet=1)
 else:
Index: pymol/modules/pmg_tk/skins/demo/__init__.py
===
--- pymol/modules/pmg_tk/skins/demo/__init__.py (revision 3896)
+++ pymol/modules/pmg_tk/skins/demo/__init__.py (working copy)
@@ -19,6 +19,8 @@
 ofile_list = askopenfilename(initialdir = self.fileOpenPath,
  filetypes=self.app.getLoadableFileTypes(),
  multiple=1) 
+# CG: work around Python/Tk bug http://bugs.python.org/issue5712
+if isinstance(ofile_list, basestring): ofile_list = [ofile_list]
 for ofile in ofile_list:
 if len(ofile):
 self.fileOpenPath = os.path.dirname(ofile)
Index: pymol/modules/pmg_tk/skins/normal/__init__.py
===
--- pymol/modules/pmg_tk/skins/normal/__init__.py   (revision 3896)
+++ pymol/modules/pmg_tk/skins/normal/__init__.py   (working copy)
@@ -538,11 +538,15 @@
 ofile_list = askopenfilename(initialdir = initdir,
  filetypes=ftypes,
  multiple=1) # new option in Tk 8.4
+# CG: work around Python/Tk bug http://bugs.python.org/issue5712
+if isinstance(ofile_list, basestring): ofile_list = [ofile_list]
 else:
 ofile_list = [ askopenfilename(initialdir = initdir,
  filetypes=ftypes) ]
 for ofile in ofile_list:
 if len(ofile):
+# CG: filenames containing whitespace
+if ofile.startswith('{'): ofile = ofile[1:-1]
 if not tutorial:
 self.initialdir = re.sub(r[^\/\\]*$,,ofile)
 try:
--
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires 
February 28th, so secure your free ArcSight Logger TODAY! 
http://p.sf.net/sfu/arcsight-sfd2d___
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] PyMOL Project Updates Open Source PyMOL v1.4b1

2011-04-01 Thread Christoph Gohlke 



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
(https://sourceforge.net/projects/pymol/files/pymol/1.4/).  I'm
calling this v1.4b1 (beta one) on the SourceForge site.

We will collect bug reports from you, the community, and then release
the stable v1.4 official code once the serious bugs are fixed.
Additionally, in order to improve communication and openness, I've
re-enabled the SourceForge bug tracker
(https://sourceforge.net/tracker/?group_id=4546atid=104546).  If
someone would like to act as a good steward and help manage the
tracker, please let me know.  This will help us stay on top of the
open-source bugs.


For those adventurous enough to try the new code please give it a
shot.  If you're not familiar with building PyMOL, please wait for the
stable v1.4 release.  For those wishing to try the new beta release
these following notes might help:

(1) If you're building from source, please install
  * glew
  * glew-devel
as they're new dependencies.  I'm using glew 1.5.8 on OpenSuSE 11.3.

(2) This update requires your hardware to support OpenGL 2.0+.  There
are known problems running this from within a VM.  I think Parallels
does handle openGL 2.0+, but VMWare does not yet support it.

(3) Please update your video card drivers.  My build just failed to
compile shaders (at run time) because I had the wrong drivers
installed!

(4) Volumes don't yet ray trace, but they will soon.  For a nice
image, set use_shaders and also try,
   Display  Quality  Maximum Quality
before using the png command to save the image.

(5) cealign is properly integrated and memory leaks and crashing
should be fixed.

(6) I only made changes to the Linux portion of the setup.sh file.  If
you're daring enough on Mac/Fink feel free to try get the build
working there, too.

(7) The 'svn diff' from the last revision is 12000+ lines long, so
there's quite a few changes.

Cheers,

-- Jason




Thank you. It builds and works well on Windows after removing stdafx.h 
from layer5/main.c.


Christoph
Index: layer5/main.c
===
--- layer5/main.c   (revision 3938)
+++ layer5/main.c   (working copy)
@@ -23,7 +23,6 @@
 #ifdef WIN32
 #include signal.h
 #include tchar.h
-#include stdafx.h
 #endif

 /* END PROPRIETARY CODE SEGMENT */
--
Create and publish websites with WebMatrix
Use the most popular FREE web apps or write code yourself; 
WebMatrix provides all the features you need to develop and 
publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
___
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] global illumination, volume representation and ipython

2011-04-11 Thread Christoph Gohlke 


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 to the open-source branch.

 Cheers,

 -- Jason


Building the open-source branch currently fails with

PyMOL.obj : error LNK2019: unresolved external symbol 
_ExecutiveGetObjectNames referenced in function _PyMOL_CmdGetNames
build\lib.win32-2.6\pymol\_cmd.pyd : fatal error LNK1120: 1 unresolved 
externals

This refers to line 4473 in layer5\PyMol.c.

Thanks,

Christoph

--
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
___
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] Open Source PyMOL v1.5.0.1

2012-02-13 Thread Christoph Gohlke 
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.

 Cheers,

 -- Jason

 On Mon, Feb 13, 2012 at 3:47 PM, Christoph Gohlkecgoh...@uci.edu  wrote:


 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 this is accessible form the
 PyMOL project page on SourceForge
 (http://sourceforge.net/projects/pymol/).

 Before upgrading PyMOL -- please -- upgrade your video drivers! NVidia
 and AMD/ATI cards are known to work well. But, Intel Mobile and other
 low-end cards might have issues with the new rendering. The majority
 of rendering anomalies are fixed by simply upgrading your video
 drivers.

 You should be able to pull and build just like normal. You will need Python 
 2.7.

 Some simple testing on my Linux machine shows the following
 improvements in real-time rendering performance for a large protein
 (58,000 atom Gro-EL, PDB 1AON) with the new open-source PyMOL code:

 Lines:
  240% increase (81 FPS to 270 FPS)
 Spheres:
  864% increase (28 FPS to 270 FPS)
 Sticks:
  2100% increase (8 FPS to 180 FPS)
 Cartoon:
  3757% increase (27 to 270 FPS)
 Surface:
  2600% increase (10 to 270 FPS)
 Mesh:
  33% (180 FPS to 270 FPS)

 Your numbers will be different. This Linux machine has a powerful card
 used for development
 (http://www.amd.com/us/products/workstation/graphics/ati-firepro-3d/v8800/Pages/v8800.aspx).
 It was generously donated by AMD. If you use an AMD/ATI card and PyMOL
 works for you it's because AMD/ATI helped out. You may want to thank
 them. What I've seen is that the more powerful your card the greater
 the _difference_ in speed. That is, low-end cards should see
 improvements in the range of tens to hundreds of percent while more
 powerful cards should register improvements like mine, in the
 thousands of percent for some representations.

 To quickly test performance of the new code on your machine just load
 a large structure (eg. 1AON; 3R8O and 3R8T) and quickly
 rotate/translate it. To see the refresh rate, type set
 show_frame_rate. The refresh rate shows up in the lower right hand
 corner. Compare the frame rate, smoothness, and rendering quality when
 the setting use_shaders is turned off and when it's turned on.
 Compare different representations, each time turning on and off the
 use_shaders setting.

 You can quickly update old PyMOL session files to the new rendering by
 clicking, SettingsRenderingModernize after loading the old
 session file. PyMOL will flip all the right settings to update
 rendering. If the new code doesn't render properly, you can revert to
 the old style rendering by typing:

set use_shaders, 0

set sphere_mode, 0


 Please let us know how it goes.

 Cheers,

 -- Jason, Blainethe PyMOL Team


 That's good news! Thank you!

 It seems that several new files, which are included in the bz2
 distribution, are missing in svn trunk. For example
 create_shadertext.py, modules\pymol\constants_palette.py and some files
 in data\shaders.

 http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/

 Christoph

 --
 Try before you buy = See our experts in action!
 The most comprehensive online learning library for Microsoft developers
 is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
 Metro Style Apps, more. Free future releases when you subscribe now!
 http://p.sf.net/sfu/learndevnow-dev2
 ___
 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




--
Try before you buy = See our experts in action!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-dev2
___
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] PyMOL 1.6 pre-release announcement

2013-03-25 Thread Christoph Gohlke 

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 drawing. For non-integrated chipsets this typically means higher 
quality and quicker rendering.

Please also note that the URL of the SVN repository changed due to an upgrade 
of the SourceForge website:

   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol

As always, we welcome bug reports and positive feedback.

Cheers,

- The PyMOL Team at Schrödinger



Hello,

Please consider the attached changes for building with msvc on Windows.

Also, the latest changes to vmdir.h don't compile with msvc.
http://sourceforge.net/p/pymol/code/4025/tree//trunk/pymol/contrib/uiuc/plugins/molfile_plugin/src/vmddir.h?diff=50c0fc56e88f3d0bdf694277:4024

Opening absolute paths does not work on Windows (e.g. C:\1bna.pdb):

Index: pymol/modules/pymol/internal.py
===
--- pymol/modules/pymol/internal.py (revision 4025)
+++ pymol/modules/pymol/internal.py (working copy)
@@ -303,7 +303,7 @@
 try:
 if not isinstance(finfo, basestring):
 handle = finfo
-elif ':' in finfo:
+elif '://' in finfo:
 import urllib
 handle = urllib.urlopen(finfo)
 else:


The launch script, Scripts\pymol.bat, seems overly complicated and 
doesn't always work for binary installers. Suggestion:


Index: pymol/setup.py
===
--- pymol/setup.py  (revision 4025)
+++ pymol/setup.py  (working copy)
@@ -119,9 +119,7 @@

 with open(launch_script, 'w') as out:
 if sys.platform.startswith('win'):
-out.write('set PYMOL_PATH=' + pymol_path + os.linesep)
-out.write('%s %s' % (python_exe, pymol_file))
-out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
+out.write(r'@%~dp0\..\pythonw.exe -m pymol.__init__ %*')
 else:
 out.write('#!/bin/sh' + os.linesep)
 if sys.platform.startswith('darwin'):


Thanks,

Christoph
Index: pymol/layer0/os_predef.h
===
--- pymol/layer0/os_predef.h(revision 4025)
+++ pymol/layer0/os_predef.h(working copy)
@@ -109,6 +109,7 @@
 #endif
 
 #if defined(_WIN32) || defined(_WIN64)
+#define M_PI 3.1415926535897932384626433832795
 #define fmax max
 #define fmin min
 #pragma warning (disable:4996)
Index: pymol/layer2/RepLabel.c
===
--- pymol/layer2/RepLabel.c (revision 4025)
+++ pymol/layer2/RepLabel.c (working copy)
@@ -90,12 +90,13 @@
 }
   } else if(G-HaveGUI  G-ValidContext) {
 if(pick) {
+  Pickable *p;
+  int i;
   if (I-shaderCGO){
CGORenderGLPicking(I-shaderCGO, pick, I-R.context, I-R.cs-Setting, 
I-R.obj-Setting);
return;
   }
-  Pickable *p = I-R.P;
-  int i;
+  p = I-R.P;
   SceneSetupGLPicking(G);
   if(c) {
 char *st;
Index: pymol/layer5/main.c
===
--- pymol/layer5/main.c (revision 4025)
+++ pymol/layer5/main.c (working copy)
@@ -23,7 +23,6 @@
 #ifdef WIN32
 #include signal.h
 #include tchar.h
-#include stdafx.h
 #endif
 
 /* END PROPRIETARY CODE SEGMENT */
@@ -1792,9 +1791,8 @@
 
 int main_exec(int argc, char **argv)
 {
-  is_shared = 0;
-
   PyMOLGlobals *G = SingletonPyMOLGlobals;
+  is_shared = 0;  
   myArgc = argc;
   myArgv = argv;
 
Index: pymol/modules/cealign/src/ccealignmodule.cpp
===
--- pymol/modules/cealign/src/ccealignmodule.cpp(revision 4025)
+++ pymol/modules/cealign/src/ccealignmodule.cpp(working copy)
@@ -631,11 +631,11 @@
   int m = (int) v.dim1();
   int n = (int) v.dim2();

-  TA2double rVal(n,m);
+  TA2double rVal((int)n,(int)m);

   for ( int i = 0; i  m; i++ )
 for ( int j = 0; j  n; j++ )
-  rVal[j][i] = v[i][j];
+  rVal[(int)j][(int)i] = v[(int)i][(int)j];

   return rVal;
 }
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
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] plugin errors in pymol 1.7.2.1

2014-12-20 Thread Christoph Gohlke 
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
 http://openbabel.org/wiki/Get_Open_Babel). As far as I know for
 Windows there is not a 64 bit version of OpenBabel and hence if you want
 to use openbabel and optimize plugin on a 64 bit Windows you have to
 instal the 32-bit version of Python and PyMOL.

 Regards,
 Osvaldo.


 On Sat, Dec 20, 2014 at 4:08 PM, Hena Dutta hdutt...@gmail.com
 mailto:hdutt...@gmail.com wrote:

 Dear Pymol Users,
 I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some
 errors. Please see the highlighted portion below.

 How can I see stereo, although it has been enabled?
 I installed Openbabel, but some plug-in are not being initialized.
 Could you please suggest how can I solve these problems?

 Best regards,
 Hena


 After running the program I found some
 PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
   Copyright (c) Schrodinger, LLC.
   All Rights Reserved.

  Created by Warren L. DeLano, Ph.D.

  PyMOL is user-supported open-source software.  Although some
 versions
  are freely available, PyMOL is not in the public domain.

  If PyMOL is helpful in your work or study, then please volunteer
  support for our ongoing efforts to create open and affordable
 scientific
  software by purchasing a PyMOL Maintenance and/or Support
 subscription.

  More information can be found at http://www.pymol.org;.

  Enter help for a list of commands.
  Enter help command-name for information on a specific command.

   Hit ESC anytime to toggle between text and graphics.

   Detected OpenGL version 2.0 or greater. Shaders available.
   Detected GLSL version 4.40.
   OpenGL graphics engine:
GL_VENDOR:   NVIDIA Corporation
GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
GL_VERSION:  4.4.0 NVIDIA 344.60
   Detected 8 CPU cores.  Enabled multithreaded rendering.



 OpenGL quad-buffer stereo 3D detected and enabled.
   Executive: Loading version 1.600 session...
 Unable to initialize plugin 'mtsslDockGui'
 (pmg_tk.startup.mtsslDockGui).
 
 

 Optimize plug-in needs openbabel to be installed in your system,
 please follow the instructions at
 http://openbabel.org/wiki/Get_Open_Babel

 
 
 Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
 Unable to initialize plugin 'mtsslTrilaterate'
 (pmg_tk.startup.mtsslTrilaterate).

 
 --
 Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
 from Actuate! Instantly Supercharge Your Business Reports and Dashboards
 with Interactivity, Sharing, Native Excel Exports, App Integration 
 more
 Get technology previously reserved for billion-dollar corporations, FREE
 
 http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net
 mailto: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




 --
 Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
 from Actuate! Instantly Supercharge Your Business Reports and Dashboards
 with Interactivity, Sharing, Native Excel Exports, App Integration  more
 Get technology previously reserved for billion-dollar corporations, FREE
 http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/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


--
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration  more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/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

Re: [PyMOL] plugin errors in pymol 1.7.2.1

2014-12-20 Thread Christoph Gohlke 
The optimize plugin loads and seems to work, i.e. it runs and produces 
some output that looks reasonable. Is there a proper test for the 
plugin? I tried to compare results to pymol on Ubuntu 14.10 but that 
version is unstable...

Christoph


On 12/20/2014 3:32 PM, Osvaldo Martin wrote:
 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, Christoph Gohlke cgoh...@uci.edu
 mailto:cgoh...@uci.edu wrote:

 Try the 64 bit version of OpenBabel at
 http://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel
 http://www.lfd.uci.edu/%7Egohlke/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
  http://openbabel.org/wiki/Get_Open_Babel). As far as I know for
  Windows there is not a 64 bit version of OpenBabel and hence if you want
  to use openbabel and optimize plugin on a 64 bit Windows you have to
  instal the 32-bit version of Python and PyMOL.
 
  Regards,
  Osvaldo.
 
 
  On Sat, Dec 20, 2014 at 4:08 PM, Hena Dutta hdutt...@gmail.com 
 mailto:hdutt...@gmail.com
  mailto:hdutt...@gmail.com mailto:hdutt...@gmail.com wrote:
 
  Dear Pymol Users,
  I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some
  errors. Please see the highlighted portion below.
 
  How can I see stereo, although it has been enabled?
  I installed Openbabel, but some plug-in are not being initialized.
  Could you please suggest how can I solve these problems?
 
  Best regards,
  Hena
 
 
  After running the program I found some
  PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
 
   Created by Warren L. DeLano, Ph.D.
 
   PyMOL is user-supported open-source software.  Although some
  versions
   are freely available, PyMOL is not in the public domain.
 
   If PyMOL is helpful in your work or study, then please 
 volunteer
   support for our ongoing efforts to create open and affordable
  scientific
   software by purchasing a PyMOL Maintenance and/or Support
  subscription.
 
   More information can be found at http://www.pymol.org;.
 
   Enter help for a list of commands.
   Enter help command-name for information on a specific 
 command.
 
Hit ESC anytime to toggle between text and graphics.
 
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.40.
OpenGL graphics engine:
 GL_VENDOR:   NVIDIA Corporation
 GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
 GL_VERSION:  4.4.0 NVIDIA 344.60
Detected 8 CPU cores.  Enabled multithreaded rendering.
 
 
 
  OpenGL quad-buffer stereo 3D detected and enabled.
Executive: Loading version 1.600 session...
  Unable to initialize plugin 'mtsslDockGui'
  (pmg_tk.startup.mtsslDockGui).
  
 
 
  Optimize plug-in needs openbabel to be installed in your system,
  please follow the instructions at
 http://openbabel.org/wiki/Get_Open_Babel
 
  
 
  Unable to initialize plugin 'mtsslWizard' 
 (pmg_tk.startup.mtsslWizard).
  Unable to initialize plugin 'mtsslTrilaterate'
  (pmg_tk.startup.mtsslTrilaterate).
 
  
 --
  Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
  from Actuate! Instantly Supercharge Your Business Reports and 
 Dashboards
  with Interactivity, Sharing, Native Excel Exports, App Integration 
  more
  Get technology previously reserved for billion-dollar corporations, 
 FREE
 
 http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk
  ___
  PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net
 mailto:PyMOL-users@lists.sourceforge.net
  mailto:PyMOL-users@lists.sourceforge.net
 mailto: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
 
 
 
 
  
 --
  Download BIRT iHub F-Type - The Free

Re: [PyMOL] PyMOL installation on Windows 7

2015-03-13 Thread Christoph Gohlke 
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-1.7.2.1-cp27-none-win_amd64.whl
   pymol_launcher-1.0-cp27-none-win_amd64.whl

Then run this command from the folder containing the downloaded.whl files:

C:\Python27\python.exe pip-6.0.8-py2.py3-none-any.whl/pip install 
--no-index --find-links=%CD% pymol_launcher

Christoph


On 3/13/2015 4:17 AM, Brenton Horne wrote:
 Oh, I have something else. Running in command prompt in admin mode I
 receive this error when running these whl installation commands:

 Traceback (most recent call last):
File C:\Python27\lib\runpy.py, line 162, in _run_module_as_main
  __main__, fname, loader, pkg_name)
File C:\Python27\lib\runpy.py, line 72, in _run_code
  exec code in run_globals
File C:\Python27\Scripts\pip2.exe\__main__.py, line 5, in module
 ImportError: No module named pip

 On 13/03/2015 9:04 PM, Brenton Horne wrote:
 Hi,

 I have tried installing PyMOL via pip  wheel files (found here
 http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol) using python 2.7.9
 and while no obvious errors occurred during the execution of the |pip
 install ...| commands I have no new files in |C:\Python27|, my python
 directory. I have allowed for the fact that pip for me is at
 |C:\Python27\Scripts\pip2.exe| instead of
 |C:\Python27\Scripts\pip.exe| like I understand it usually is, as far
 as adjusting the PYTHONPATH variable accordingly. Any ideas on how to
 install PyMOL on my 64 bit Windows 7 SP1 OS? I have VisualStudio 2010
 installed on my PC if relevant. If you need any other details please ask!

 Thanks for your time,
 Brenton


 --
 Dive into the World of Parallel Programming The Go Parallel Website, 
 sponsored
 by Intel and developed in partnership with Slashdot Media, is your hub for 
 all
 things parallel software development, from weekly thought leadership blogs to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now.http://goparallel.sourceforge.net/


 ___
 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



 --
 Dive into the World of Parallel Programming The Go Parallel Website, sponsored
 by Intel and developed in partnership with Slashdot Media, is your hub for all
 things parallel software development, from weekly thought leadership blogs to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now. http://goparallel.sourceforge.net/



 ___
 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


--
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the 
conversation now. http://goparallel.sourceforge.net/
___
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] Problem with pymol installation

2016-03-21 Thread Christoph Gohlke 
Make sure you are using the 64-bit version of Python 2.7: 
python-2.7.11.amd64.msi.

If that does not help, please list the contents of %CD%: dir "%CD%"\*.whl

Christoph



On 3/21/2016 3:31 AM, Bondurant wrote:
> Hi everybody,
> I recently restored my laptop to factory settings and I am trying now to
> install latest precompiled pymol version  following the instructions
> from http://www.pymolwiki.org/index.php/Windows_Install.
> I have installed python 2.7.11 and put in a Pymol_installation folder
> pip 8.0.3, numpy 1.10.4+mkl, pmw 2.0.1, pymol 1.8.1.0 and pymol_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 the following error:
>
>   "Could not find  a version that satifisfies the requirement
> pymol-launcher (from versions: )
> No matching distribution found for pymol launcher"
>
>
> Could you provide me any help? Am i doing anything wrong? Have i skipped
> any step in the installation process?
>
> Thanks
>
> Sergio
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140
>
>
>
> ___
> 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
>

--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140
___
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] Unofficial Windows PyMOL Binaries fails to run

2017-02-13 Thread Christoph Gohlke 
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 Python3.6.0 and then, in a command line prompt run as
> administrator, I typed:
>
> python -m pip install --upgrade pip
> python -m pip install --upgrade wheel
>
> python -m pip install "numpy-1.12.0+mkl-cp36-cp36m-win_amd64.whl"
> python -m pip install Pmw-2.0.1-py3-none-any.whl
> python -m pip install pymol-1.8.5.0-cp36-cp36m-win_amd64.whl
> python -m pip install pymol_launcher-1.0-cp36-cp36m-win_amd64.whl
>
> Similarly, I installed Python3.5.3 and then I typed:
>
> python -m pip install --upgrade pip
> python -m pip install --upgrade wheel
>
> python -m pip install "numpy-1.12.0+mkl-cp35-cp35m-win_amd64.whl"
> python -m pip install Pmw-2.0.1-py3-none-any.whl
> python -m pip install pymol-1.8.5.0-cp35-cp35m-win_amd64.whl
> python -m pip install pymol_launcher-1.0-cp35-cp35m-win_amd64.whl
>
> In both cases, a C:\Program Files\Python3*\PyMOL.exe was produced.
> Nevertheless, this executable did nothing when I ran it. It did not even
> produce any error message that could guide me!
>
> On the contrary, when I followed the same approach for Python2.7.13:
>
> python -m pip install --upgrade pip
> python -m pip install --upgrade wheel
>
> python -m pip install "numpy-1.12.0+mkl-cp27-cp27m-win_amd64.whl"
> python -m pip install Pmw-2.0.1-py2-none-any.whl
> python -m pip install pymol-1.8.5.0-cp27-cp27m-win_amd64.whl
> python -m pip install pymol_launcher-1.0-cp27-cp27m-win_amd64.whl
>
> a fully functional C:\Python27\PyMOL.exe was produced.
>
> The reason I do not want to stick to Python27 is that Python27-based PyMOL
> binaries for the newest versions of PyMOL are no longer produced for
> 32-bit Windows which are still in use by some of my students. I want all
> students to run the same PyMOL version, regardless of their Windows system
> type.
>
> I would be indebted if you could point out to me what I do wrong.
>
> Thank you in advance.
>
> Yours Sincerely,
>
> Dr Ioannis Michalopoulos
>

Install the "Microsoft Visual C++ 2015 Redistributable" 
?

If that does not work, start pymol on a command line via `python.exe -m 
pymol` to get a traceback.

Christoph

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
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] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

2017-08-21 Thread Christoph Gohlke 

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 wrote:

Dear PyMOL Users
Today, I installed PyMOL 1.8.7 with Python 3.6 on Windows 10. But,
unfortunatelt facing one issue with Plugin Manager. The error is as
following:

Error: 1
TypeError Exception in Tk callback
   Function: .plugin_manager
at 0x019192E818C8> (type: )
   Args: ()
Traceback (innermost last):
   File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py",
line 1776, in __call__
 return self.func(*args)
   File "C:\Python36\lib\site-packages\pymol\plugins\legacysupport.py",
line 73, in plugin_manager
 managergui.manager_dialog()
   File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
line 47, in manager_dialog
 dialog = PluginManager(get_tk_root())
   File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
line 129, in __init__
 notebook = Pmw.NoteBook(master)
   File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
line 60, in __init__
 Pmw.Color.bordercolors(self, self['hull_background'])
   File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
line 359, in bordercolors
 '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),

Any solution?
Thanks in advance.
From
Vijay



--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
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] Windows PDB file for debugging pymol C extension?

2018-05-09 Thread Christoph Gohlke 
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 extension part 
(_cmd.cp36-win_amd64.pyd) using pymol open source 2.1.0. I'd like to 
debug it; is there a symbol file (.pdb) available anywhere? Or failing 
that, can I rebuild the C extension from source and create a pdb?


--
Gary Oberbrunner


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
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] Windows PDB file for debugging pymol C extension?

2018-05-09 Thread Christoph Gohlke 
Try to turn on heap verification for python.exe using the following 
registration key and then start pymol with `python.exe -m pymol`


[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image 
File Execution Options\python.exe]

"GlobalFlag"="0x0200"
"VerifierFlags"=dword:0001
"PageHeapFlags"="0x3"


Christoph


On 5/9/2018 5:32 PM, Gary Oberbrunner wrote:
Thanks -- unfortunately it seems to be heap corruption. I can see where 
it's detected:


         ntdll.dll!RtlpLogHeapFailure ()Unknown
ntdll.dll!RtlFreeHeap()Unknown
ucrtbase.dll!_free_base()Unknown
_cmd.cp36-win_amd64.pyd!VLAFree(void * ptr) Line 222C++
_cmd.cp36-win_amd64.pyd!CGOFreeImpl(CGO * I, short withVBOs) Line 447C++
_cmd.cp36-win_amd64.pyd!CGOFree(CGO * & I) Line 435C++
_cmd.cp36-win_amd64.pyd!OrthoInvalidateDoDraw(_PyMOLGlobals * 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, 2018 at 1:54 PM, Christoph Gohlke <cgoh...@uci.edu 
<mailto:cgoh...@uci.edu>> wrote:


I put a VS2015 build of svn rev 4189 including debug information
files for the pymol source at
<https://www.lfd.uci.edu/~gohlke/download/pymol-svn-4189.zip
<https://www.lfd.uci.edu/%7Egohlke/download/pymol-svn-4189.zip>>

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
extension part (_cmd.cp36-win_amd64.pyd) using pymol open source
2.1.0. I'd like to debug it; is there a symbol file (.pdb)
available anywhere? Or failing that, can I rebuild the C
extension from source and create a pdb?

-- 
Gary Oberbrunner




--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net
<mailto:PyMOL-users@lists.sourceforge.net>)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
<https://lists.sourceforge.net/lists/listinfo/pymol-users>
Archives:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net
<http://www.mail-archive.com/pymol-users@lists.sourceforge.net>




--
Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
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] Problem In using Pymol 2.4 through IDLE -Python 3

2020-10-23 Thread Christoph Gohlke 
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 2.4 (Python 3.7) on Windows 10 (64 bit).
It strated without any problem when the icon was double clicked.But when 
I tried to use it from IDLE (PYTHON 3.7- 64bit), it showed following error:

"ImportError: DLL load failed: The specified module could not be found."

To find a solution, I installed Pymol 2.4 with Python 3.8, but Pymol did 
not start at all. Then, I tried Pymol 2.4 with Python 3.9 also, again 
PyMOL 2.4 did not start at all.
Finally, I tried Python 2.7 (using PyMOL 2.0), it worked perfectly and 
was running from IDLE, as well.


I need help to remove the error
"ImportError: DLL load failed: The specified module could not be found."
to run PyMOL 2.4 with Python 3 using IDLE?

Thanks in advance.

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/ 





___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Scroll wheel not slabbing

2021-05-02 Thread Christoph Gohlke 
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 mouse scroll wheel not doing anything when I move PyMOL to the 
external screen of my laptop,  ie. I get no slabbing in viewing mode. 
Moving PyMOL back to the laptop screen restores scrolling and it seems 
to happen only when I used extended desktop - duplicate screen or 
external only work fine. Any idea what could be the issue? A bit of a 
pain as I prefer the external screen for mol graphics.


My old version 1.8.2 works correctly.

Also Plugin manager does seem to work. Seem to get a lot of errors 
related to Pmw (which is up to date). Any ideas? Errors below.


cheers, Marko


TypeError Exception in Tk callback
   Function: .plugin_manager 
at 0x0234B6DCDCA0> (type: )

   Args: ()
Traceback (innermost last):
   File "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py", 
line 1776, in __call__

     return self.func(*args)
   File "C:\Python39\lib\site-packages\pymol\plugins\legacysupport.py", 
line 87, in plugin_manager

     managergui.manager_dialog()
   File "C:\Python39\lib\site-packages\pymol\plugins\managergui.py", 
line 47, in manager_dialog

     dialog = PluginManager(get_tk_root())
   File "C:\Python39\lib\site-packages\pymol\plugins\managergui.py", 
line 129, in __init__

     notebook = Pmw.NoteBook(master)
   File 
"C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py", line 
60, in __init__

     Pmw.Color.bordercolors(self, self['hull_background'])
   File "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py", 
line 359, in bordercolors

     '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
TypeError: %x format: an integer is required, not float

--

Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@cam.ac.uk
+44 (0)1223 766 044
@HyvonenGroup
http://hyvonen.bioc.cam.ac.uk
  




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe