From: Thomas H. <tho...@sc...> - 2013-03-24 10:02:18
|
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 -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Michael B. <mb...@de...> - 2013-03-24 12:19:00
|
Hi, On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote: > 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. Great! Is there some pre-release version number assigned to that commit, like "1.6.0pre1" or "1.6.0rc1", assuming a final 1.6.0 will follow at some point? Best regards, Michael |
From: Thomas H. <tho...@sc...> - 2013-03-24 18:49:11
|
Hi Michael, I haven't tagged that commit. It's svn revision 4025. For the final 1.6.0 version we will upload a tar.gz archive to sourceforge. Cheers, Thomas On Mar 24, 2013, at 1:18 PM, Michael Banck <mb...@de...> wrote: > Hi, > > On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote: >> 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. > > Great! Is there some pre-release version number assigned to that > commit, like "1.6.0pre1" or "1.6.0rc1", assuming a final 1.6.0 will > follow at some point? > > Best regards, > > Michael -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Michael B. <mb...@de...> - 2013-03-25 16:11:49
|
Hi, On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote: > 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. [...] > As always, we welcome bug reports and positive feedback. Works fine for me so far, I noticed one thing though: In Wizard -> Demo -> Sculpting, the protein backbone mostly disappears if I rotate a bond, I just see the angle and the spheres, while the backbone is almost invisible. This does not seem to happen if I rotate around a bond at the outside of the protein. In 1.5.0.1, the appearance does not change between dragging atoms and rotating bonds which made it easier to rotate around bonds. This is with a Lenovo T400 and internal Intel Graphics. Michael |
From: Christoph G. <cg...@uc...> - 2013-03-25 17:11:51
Attachments:
pymol_r4025.diff
|
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 |
From: Thomas H. <tho...@sc...> - 2013-03-25 21:52:41
|
Hi Christoph, thanks a lot for the patches. Regarding your suggestion for pymol.bat: I guess this will not work if you install with a custom prefix, since you make assumptions where to find pythonw.exe and the pymol module. I suggest to discuss this off-list, since it's quite specific. Cheers, Thomas Christoph Gohlke wrote, On 03/25/13 18:11: > 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 -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Stephen P. M. <s.m...@sb...> - 2013-03-25 17:32:04
|
On Sun, 24 Mar 2013 11:02:08 +0100 Thomas Holder <tho...@sc...> 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 > I managed to download the source code. There were a lot of warnings during the compilation and I got the following error message: usr/include/python2.7 -c layer1/TypeFace.c -o build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error: ft2build.h: No such file or directory compilation terminated. I don't have the faintest idea as to what supplies ft2build.h and would appreciate a point in the correct direction. Thanks in advance. |
From: Michael B. <mb...@de...> - 2013-03-25 17:47:46
|
Hi Stephen, On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote: > On Sun, 24 Mar 2013 11:02:08 +0100 > Thomas Holder <tho...@sc...> wrote: > > 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 > > > > I managed to download the source code. There were a lot of warnings > during the compilation and I got the following error message: > > usr/include/python2.7 -c layer1/TypeFace.c -o > build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math > -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error: > ft2build.h: No such file or directory compilation terminated. > > I don't have the faintest idea as to what supplies ft2build.h and would > appreciate a point in the correct direction. It's shipped by the libfreetype development package. Michael |
From: Stephen P. M. <s.m...@sb...> - 2013-03-25 19:03:17
|
On Mon, 25 Mar 2013 18:47:27 +0100 Michael Banck <mb...@de...> wrote: > Hi Stephen, > > On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote: > > On Sun, 24 Mar 2013 11:02:08 +0100 > > Thomas Holder <tho...@sc...> wrote: > > > 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 > > > > > > > I managed to download the source code. There were a lot of warnings > > during the compilation and I got the following error message: > > > > usr/include/python2.7 -c layer1/TypeFace.c -o > > build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math > > -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error: > > ft2build.h: No such file or directory compilation terminated. > > > > I don't have the faintest idea as to what supplies ft2build.h and > > would appreciate a point in the correct direction. > > It's shipped by the libfreetype development package. > > > Michael > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pym...@li... Many thanks, That solved the problem! v1.6.0 is now compiled and installed. |
From: David H. <li...@co...> - 2013-04-26 23:43:09
|
Hi Thomas, I'm running into issues with color compatibility between 1.6 and earlier versions when opening pses (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: Setting-Error: type read mismatch (color) 6 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 664 (b) background color disparity: saved in 1.5 with black background; opens in 1.6 with a white background saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red background These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, others who would like to beta test can use devel:languages:python repo in openSUSE: https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython -David On Sun, Mar 24, 2013 at 6:02 AM, Thomas Holder <tho...@sc...> 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 > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Robert C. <rob...@qu...> - 2013-06-14 19:23:45
|
Hello Thomas and David, Was there any resolution of this? I've just compiled the latest version from SVN and I have the same problem opening files created under version 1.5.0. This is on Debian testing (32-bit). Cheers, Rob On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> wrote: > Hi Thomas, > > I'm running into issues with color compatibility between 1.6 and > earlier versions when opening pses > (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: > Setting-Error: type read mismatch (color) 6 > Setting-Error: type read mismatch (color) 663 > Setting-Error: type read mismatch (color) 664 > (b) background color disparity: > saved in 1.5 with black background; opens in 1.6 with a white background > saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red > background > > These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, > others who would like to beta test can use devel:languages:python repo > in openSUSE: > https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython > > -David > -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Thomas H. <tho...@sc...> - 2013-06-15 08:45:26
|
Hi Rob, this has not been fixed yet, I'm really sorry. We'll look into this ASAP. It only affects the open-source code, apparently we missed something when syncing with the incentive codebase. Cheers, Thomas On Jun 14, 2013, at 9:23 PM, Robert Campbell <rob...@qu...> wrote: > Hello Thomas and David, > > Was there any resolution of this? I've just compiled the latest version > from SVN and I have the same problem opening files created under version > 1.5.0. This is on Debian testing (32-bit). > > Cheers, > Rob > > On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> > wrote: > >> Hi Thomas, >> >> I'm running into issues with color compatibility between 1.6 and >> earlier versions when opening pses >> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: >> Setting-Error: type read mismatch (color) 6 >> Setting-Error: type read mismatch (color) 663 >> Setting-Error: type read mismatch (color) 664 >> (b) background color disparity: >> saved in 1.5 with black background; opens in 1.6 with a white background >> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red >> background >> >> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, >> others who would like to beta test can use devel:languages:python repo >> in openSUSE: >> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython >> >> -David -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Thomas H. <tho...@sc...> - 2013-06-18 11:37:51
|
This is fixed in SVN rev 4032. Cheers, Thomas Thomas Holder wrote, On 06/15/13 10:45: > Hi Rob, > > this has not been fixed yet, I'm really sorry. We'll look into this > ASAP. It only affects the open-source code, apparently we missed > something when syncing with the incentive codebase. > > Cheers, > Thomas > > On Jun 14, 2013, at 9:23 PM, Robert Campbell <rob...@qu...> wrote: >> Hello Thomas and David, >> >> Was there any resolution of this? I've just compiled the latest version >> from SVN and I have the same problem opening files created under version >> 1.5.0. This is on Debian testing (32-bit). >> >> Cheers, >> Rob >> >> On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> >> wrote: >> >>> Hi Thomas, >>> >>> I'm running into issues with color compatibility between 1.6 and >>> earlier versions when opening pses >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: >>> Setting-Error: type read mismatch (color) 6 >>> Setting-Error: type read mismatch (color) 663 >>> Setting-Error: type read mismatch (color) 664 >>> (b) background color disparity: >>> saved in 1.5 with black background; opens in 1.6 with a white background >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red >>> background >>> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, >>> others who would like to beta test can use devel:languages:python repo >>> in openSUSE: >>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython >>> >>> -David -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: David H. <li...@co...> - 2013-06-19 21:45:12
|
I still have this problem: session saved in 1.6 with a black background; opens in 1.5 (and earlier) with a red background Many of my collaborators use old versions of pymol, frequently installed onto their machines when they were bought X years ago, and this essentially makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at least not without getting weird e-mails asking why I have a sudden affinity for the color red). -David On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder < tho...@sc...> wrote: > This is fixed in SVN rev 4032. > > Cheers, > Thomas > > Thomas Holder wrote, On 06/15/13 10:45: > > Hi Rob, > > > > this has not been fixed yet, I'm really sorry. We'll look into this > > ASAP. It only affects the open-source code, apparently we missed > > something when syncing with the incentive codebase. > > > > Cheers, > > Thomas > > > > On Jun 14, 2013, at 9:23 PM, Robert Campbell <rob...@qu...> > wrote: > >> Hello Thomas and David, > >> > >> Was there any resolution of this? I've just compiled the latest version > >> from SVN and I have the same problem opening files created under version > >> 1.5.0. This is on Debian testing (32-bit). > >> > >> Cheers, > >> Rob > >> > >> On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> > >> wrote: > >> > >>> Hi Thomas, > >>> > >>> I'm running into issues with color compatibility between 1.6 and > >>> earlier versions when opening pses > >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: > >>> Setting-Error: type read mismatch (color) 6 > >>> Setting-Error: type read mismatch (color) 663 > >>> Setting-Error: type read mismatch (color) 664 > >>> (b) background color disparity: > >>> saved in 1.5 with black background; opens in 1.6 with a white > background > >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red > >>> background > >>> > >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, > >>> others who would like to beta test can use devel:languages:python repo > >>> in openSUSE: > >>> > https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython > >>> > >>> -David > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Robert H. <ha...@st...> - 2013-06-19 22:51:37
|
That would be a problem with all programs -- unless there is a SAVE mode that is "compatible with version xxxx" (as, for example, MS Word has). One cannot expect backward compatibility, I think. Bob Hanson On Wed, Jun 19, 2013 at 4:18 PM, David Hall <li...@co...> wrote: > I still have this problem: > session saved in 1.6 with a black background; opens in 1.5 (and earlier) > with a red background > > Many of my collaborators use old versions of pymol, frequently installed > onto their machines when they were bought X years ago, and this essentially > makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at > least not without getting weird e-mails asking why I have a sudden affinity > for the color red). > > -David > > > > > On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder < > tho...@sc...> wrote: > >> This is fixed in SVN rev 4032. >> >> Cheers, >> Thomas >> >> Thomas Holder wrote, On 06/15/13 10:45: >> > Hi Rob, >> > >> > this has not been fixed yet, I'm really sorry. We'll look into this >> > ASAP. It only affects the open-source code, apparently we missed >> > something when syncing with the incentive codebase. >> > >> > Cheers, >> > Thomas >> > >> > On Jun 14, 2013, at 9:23 PM, Robert Campbell < >> rob...@qu...> wrote: >> >> Hello Thomas and David, >> >> >> >> Was there any resolution of this? I've just compiled the latest >> version >> >> from SVN and I have the same problem opening files created under >> version >> >> 1.5.0. This is on Debian testing (32-bit). >> >> >> >> Cheers, >> >> Rob >> >> >> >> On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> >> >> wrote: >> >> >> >>> Hi Thomas, >> >>> >> >>> I'm running into issues with color compatibility between 1.6 and >> >>> earlier versions when opening pses >> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: >> >>> Setting-Error: type read mismatch (color) 6 >> >>> Setting-Error: type read mismatch (color) 663 >> >>> Setting-Error: type read mismatch (color) 664 >> >>> (b) background color disparity: >> >>> saved in 1.5 with black background; opens in 1.6 with a white >> background >> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red >> >>> background >> >>> >> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, >> >>> others who would like to beta test can use devel:languages:python repo >> >>> in openSUSE: >> >>> >> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython >> >>> >> >>> -David >> >> -- >> Thomas Holder >> PyMOL Developer >> Schrödinger Contractor >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Jason V. <jas...@sc...> - 2013-06-20 12:37:02
|
Hi David, If you save a session file in the latest version of PyMOL there is never the expectation that prior versions can read that file. Such "forward compatibility" (of the older versions) is not supported. We do support, however, "backward compatibility" which is when newer versions of PyMOL read older session files. Cheers, -- Jason On Wed, Jun 19, 2013 at 4:18 PM, David Hall <li...@co...> wrote: > I still have this problem: > session saved in 1.6 with a black background; opens in 1.5 (and earlier) > with a red background > > Many of my collaborators use old versions of pymol, frequently installed > onto their machines when they were bought X years ago, and this essentially > makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at > least not without getting weird e-mails asking why I have a sudden affinity > for the color red). > > -David > > > > > On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder < > tho...@sc...> wrote: > >> This is fixed in SVN rev 4032. >> >> Cheers, >> Thomas >> >> Thomas Holder wrote, On 06/15/13 10:45: >> > Hi Rob, >> > >> > this has not been fixed yet, I'm really sorry. We'll look into this >> > ASAP. It only affects the open-source code, apparently we missed >> > something when syncing with the incentive codebase. >> > >> > Cheers, >> > Thomas >> > >> > On Jun 14, 2013, at 9:23 PM, Robert Campbell < >> rob...@qu...> wrote: >> >> Hello Thomas and David, >> >> >> >> Was there any resolution of this? I've just compiled the latest >> version >> >> from SVN and I have the same problem opening files created under >> version >> >> 1.5.0. This is on Debian testing (32-bit). >> >> >> >> Cheers, >> >> Rob >> >> >> >> On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> >> >> wrote: >> >> >> >>> Hi Thomas, >> >>> >> >>> I'm running into issues with color compatibility between 1.6 and >> >>> earlier versions when opening pses >> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: >> >>> Setting-Error: type read mismatch (color) 6 >> >>> Setting-Error: type read mismatch (color) 663 >> >>> Setting-Error: type read mismatch (color) 664 >> >>> (b) background color disparity: >> >>> saved in 1.5 with black background; opens in 1.6 with a white >> background >> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red >> >>> background >> >>> >> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, >> >>> others who would like to beta test can use devel:languages:python repo >> >>> in openSUSE: >> >>> >> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython >> >>> >> >>> -David >> >> -- >> Thomas Holder >> PyMOL Developer >> Schrödinger Contractor >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Robert H. <ha...@st...> - 2013-06-20 14:06:10
|
(yes, I meant "forward compatibility" there) Jason, in our 100+ PyMOL session files that we can now read into Jmol we have a few files that don't seem to have backward compatibility to PyMOL 1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and measurements. Should I just send them to you and/or Thomas? Bob On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees < jas...@sc...> wrote: > Hi David, > > If you save a session file in the latest version of PyMOL there is never > the expectation that prior versions can read that file. Such "forward > compatibility" (of the older versions) is not supported. We do support, > however, "backward compatibility" which is when newer versions of PyMOL > read older session files. > > Cheers, > > -- Jason > > > On Wed, Jun 19, 2013 at 4:18 PM, David Hall <li...@co...> wrote: > >> I still have this problem: >> session saved in 1.6 with a black background; opens in 1.5 (and earlier) >> with a red background >> >> Many of my collaborators use old versions of pymol, frequently installed >> onto their machines when they were bought X years ago, and this essentially >> makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at >> least not without getting weird e-mails asking why I have a sudden affinity >> for the color red). >> >> -David >> >> >> >> >> On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder < >> tho...@sc...> wrote: >> >>> This is fixed in SVN rev 4032. >>> >>> Cheers, >>> Thomas >>> >>> Thomas Holder wrote, On 06/15/13 10:45: >>> > Hi Rob, >>> > >>> > this has not been fixed yet, I'm really sorry. We'll look into this >>> > ASAP. It only affects the open-source code, apparently we missed >>> > something when syncing with the incentive codebase. >>> > >>> > Cheers, >>> > Thomas >>> > >>> > On Jun 14, 2013, at 9:23 PM, Robert Campbell < >>> rob...@qu...> wrote: >>> >> Hello Thomas and David, >>> >> >>> >> Was there any resolution of this? I've just compiled the latest >>> version >>> >> from SVN and I have the same problem opening files created under >>> version >>> >> 1.5.0. This is on Debian testing (32-bit). >>> >> >>> >> Cheers, >>> >> Rob >>> >> >>> >> On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> >>> >> wrote: >>> >> >>> >>> Hi Thomas, >>> >>> >>> >>> I'm running into issues with color compatibility between 1.6 and >>> >>> earlier versions when opening pses >>> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: >>> >>> Setting-Error: type read mismatch (color) 6 >>> >>> Setting-Error: type read mismatch (color) 663 >>> >>> Setting-Error: type read mismatch (color) 664 >>> >>> (b) background color disparity: >>> >>> saved in 1.5 with black background; opens in 1.6 with a white >>> background >>> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a >>> red >>> >>> background >>> >>> >>> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, >>> >>> others who would like to beta test can use devel:languages:python >>> repo >>> >>> in openSUSE: >>> >>> >>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython >>> >>> >>> >>> -David >>> >>> -- >>> Thomas Holder >>> PyMOL Developer >>> Schrödinger Contractor >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by Windows: >>> >>> Build for Windows Store. >>> >>> http://p.sf.net/sfu/windows-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Jason V. <jas...@sc...> - 2013-06-20 14:11:20
|
Bob, Sure, feel free to send those to Thomas. Cheers, -- Jason On Thu, Jun 20, 2013 at 9:06 AM, Robert Hanson <ha...@st...> wrote: > (yes, I meant "forward compatibility" there) > > Jason, in our 100+ PyMOL session files that we can now read into Jmol we > have a few files that don't seem to have backward compatibility to PyMOL > 1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and > measurements. Should I just send them to you and/or Thomas? > > Bob > > > > On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees < > jas...@sc...> wrote: > >> Hi David, >> >> If you save a session file in the latest version of PyMOL there is never >> the expectation that prior versions can read that file. Such "forward >> compatibility" (of the older versions) is not supported. We do support, >> however, "backward compatibility" which is when newer versions of PyMOL >> read older session files. >> >> Cheers, >> >> -- Jason >> >> >> On Wed, Jun 19, 2013 at 4:18 PM, David Hall <li...@co...>wrote: >> >>> I still have this problem: >>> session saved in 1.6 with a black background; opens in 1.5 (and earlier) >>> with a red background >>> >>> Many of my collaborators use old versions of pymol, frequently installed >>> onto their machines when they were bought X years ago, and this essentially >>> makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at >>> least not without getting weird e-mails asking why I have a sudden affinity >>> for the color red). >>> >>> -David >>> >>> >>> >>> >>> On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder < >>> tho...@sc...> wrote: >>> >>>> This is fixed in SVN rev 4032. >>>> >>>> Cheers, >>>> Thomas >>>> >>>> Thomas Holder wrote, On 06/15/13 10:45: >>>> > Hi Rob, >>>> > >>>> > this has not been fixed yet, I'm really sorry. We'll look into this >>>> > ASAP. It only affects the open-source code, apparently we missed >>>> > something when syncing with the incentive codebase. >>>> > >>>> > Cheers, >>>> > Thomas >>>> > >>>> > On Jun 14, 2013, at 9:23 PM, Robert Campbell < >>>> rob...@qu...> wrote: >>>> >> Hello Thomas and David, >>>> >> >>>> >> Was there any resolution of this? I've just compiled the latest >>>> version >>>> >> from SVN and I have the same problem opening files created under >>>> version >>>> >> 1.5.0. This is on Debian testing (32-bit). >>>> >> >>>> >> Cheers, >>>> >> Rob >>>> >> >>>> >> On Fri, 2013-04-26 19:15 EDT, David Hall <li...@co...> >>>> >> wrote: >>>> >> >>>> >>> Hi Thomas, >>>> >>> >>>> >>> I'm running into issues with color compatibility between 1.6 and >>>> >>> earlier versions when opening pses >>>> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: >>>> >>> Setting-Error: type read mismatch (color) 6 >>>> >>> Setting-Error: type read mismatch (color) 663 >>>> >>> Setting-Error: type read mismatch (color) 664 >>>> >>> (b) background color disparity: >>>> >>> saved in 1.5 with black background; opens in 1.6 with a white >>>> background >>>> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a >>>> red >>>> >>> background >>>> >>> >>>> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, >>>> >>> others who would like to beta test can use devel:languages:python >>>> repo >>>> >>> in openSUSE: >>>> >>> >>>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython >>>> >>> >>>> >>> -David >>>> >>>> -- >>>> Thomas Holder >>>> PyMOL Developer >>>> Schrödinger Contractor >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> This SF.net email is sponsored by Windows: >>>> >>>> Build for Windows Store. >>>> >>>> http://p.sf.net/sfu/windows-dev2dev >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by Windows: >>> >>> Build for Windows Store. >>> >>> http://p.sf.net/sfu/windows-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> >> -- >> Jason Vertrees, PhD >> Director of Core Modeling Products >> Schrödinger, Inc. >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |