From: zjxu <zj...@ma...> - 2011-06-16 12:48:06
|
Dear everyone, when I run a script in pymol1.4.1 on the command line: pymol -rqkc script.py. Then a lot of messages "ObjectMoleculeGuessValences(1,1): Unreasonable connectivity in heteroatom, unsuccessful in guessing valences." will be printed out on the screen in addition to the script results. It is somewhat annoying. Is there any option to turn this off? Pymol1.3 works without the above complain messages. Thanks in advance. Zhijian Xu |
From: Jason V. <jas...@sc...> - 2011-06-16 13:24:25
|
Hi Zhijian, In PyMOL v1.4 and PyMOL v1.4.1 this message will be emitted. We have changed this warning message for later versions to be released in a few months' time. If you're using the open-source code, then a rebuild from source should fix this for you. I just pushed the change to the open-source project a few moments ago. Cheers, -- Jason On Thu, Jun 16, 2011 at 8:52 AM, zjxu <zj...@ma...> wrote: > Dear everyone, > when I run a script in pymol1.4.1 on the command line: pymol -rqkc > script.py. > Then a lot of messages "ObjectMoleculeGuessValences(1,1): Unreasonable > connectivity in heteroatom, > unsuccessful in guessing valences." will be printed out on the screen > in addition to the script results. > It is somewhat annoying. Is there any option to turn this off? > Pymol1.3 works without the above complain messages. > Thanks in advance. > > Zhijian Xu > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-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 PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: zjxu <zj...@ma...> - 2011-06-16 13:38:07
|
Dear Jason, Thanks very much for the prompt reply. Yes, I compiled pymol by hand from source under Linux and I will rebuild it. Best Regards, Zhijian Xu Jason Vertrees wrote: > Hi Zhijian, > > In PyMOL v1.4 and PyMOL v1.4.1 this message will be emitted. We have > changed this warning message for later versions to be released in a > few months' time. If you're using the open-source code, then a > rebuild from source should fix this for you. I just pushed the change > to the open-source project a few moments ago. > > Cheers, > > -- Jason > > > > On Thu, Jun 16, 2011 at 8:52 AM, zjxu <zj...@ma...> wrote: > >> Dear everyone, >> when I run a script in pymol1.4.1 on the command line: pymol -rqkc >> script.py. >> Then a lot of messages "ObjectMoleculeGuessValences(1,1): Unreasonable >> connectivity in heteroatom, >> unsuccessful in guessing valences." will be printed out on the screen >> in addition to the script results. >> It is somewhat annoying. Is there any option to turn this off? >> Pymol1.3 works without the above complain messages. >> Thanks in advance. >> >> Zhijian Xu >> >> ------------------------------------------------------------------------------ >> EditLive Enterprise is the world's most technically advanced content >> authoring tool. Experience the power of Track Changes, Inline Image >> Editing and ensure content is compliant with Accessibility Checking. >> http://p.sf.net/sfu/ephox-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: zjxu <zj...@ma...> - 2011-06-16 14:20:18
|
Dear Jason, I am afraid the change did not work for me. Is there anything wrong in my rebuild process? (1) I download the source code with the command: svn co https://pymol.svn.sourceforge.net/svnroot/pymol pymol (2) go to pymol/trunk/pymol, and see the ChangeLog: 2011-06-16 Jason Vertrees <Jas...@sc...> * suppress guess valences warning message to Blather (3) In pymol/trunk/pymol: python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ python setup2.py install ./pymol However, when I load a pdb, the warning comes again. "pymol -rkqc script.py" complains again. Best Regards, Zhijian Xu zjxu wrote: > Dear Jason, > Thanks very much for the prompt reply. > Yes, I compiled pymol by hand from source under Linux and I will rebuild it. > > Best Regards, > Zhijian Xu > > Jason Vertrees wrote: > >> Hi Zhijian, >> >> In PyMOL v1.4 and PyMOL v1.4.1 this message will be emitted. We have >> changed this warning message for later versions to be released in a >> few months' time. If you're using the open-source code, then a >> rebuild from source should fix this for you. I just pushed the change >> to the open-source project a few moments ago. >> >> Cheers, >> >> -- Jason >> >> >> >> On Thu, Jun 16, 2011 at 8:52 AM, zjxu <zj...@ma...> wrote: >> >> >>> Dear everyone, >>> when I run a script in pymol1.4.1 on the command line: pymol -rqkc >>> script.py. >>> Then a lot of messages "ObjectMoleculeGuessValences(1,1): Unreasonable >>> connectivity in heteroatom, >>> unsuccessful in guessing valences." will be printed out on the screen >>> in addition to the script results. >>> It is somewhat annoying. Is there any option to turn this off? >>> Pymol1.3 works without the above complain messages. >>> Thanks in advance. >>> >>> Zhijian Xu >>> >>> ------------------------------------------------------------------------------ >>> EditLive Enterprise is the world's most technically advanced content >>> authoring tool. Experience the power of Track Changes, Inline Image >>> Editing and ensure content is compliant with Accessibility Checking. >>> http://p.sf.net/sfu/ephox-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... >>> >>> >>> >> >> >> > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-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: Thomas H. <sp...@us...> - 2011-06-16 15:27:09
|
On 06/16/2011 04:24 PM, zjxu wrote: > (3) In pymol/trunk/pymol: > python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ > python setup2.py install > ./pymol > However, when I load a pdb, the warning comes again. "pymol -rkqc > script.py" complains again. have you set PYTHONPATH before running setup2.py and ./pymol? modules=/BioSoft/pymol1.4.1_2011-6-16/lib/python*/site-packages export PYTHONPATH=$modules:$PYTHONPATH python setup2.py install ./pymol If you have another (global) PyMOL installation which can be found by python, the launcher will use that one! (this could be improved I guess). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology |
From: zjxu <zj...@ma...> - 2011-06-17 01:22:54
|
Dear Thomas, It works now after taking your advice. Thanks very much. Best Regards, Zhijian Xu Thomas Holder wrote: > On 06/16/2011 04:24 PM, zjxu wrote: >> (3) In pymol/trunk/pymol: >> python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ >> python setup2.py install >> ./pymol >> However, when I load a pdb, the warning comes again. "pymol -rkqc >> script.py" complains again. > > have you set PYTHONPATH before running setup2.py and ./pymol? > > modules=/BioSoft/pymol1.4.1_2011-6-16/lib/python*/site-packages > export PYTHONPATH=$modules:$PYTHONPATH > python setup2.py install > ./pymol > > If you have another (global) PyMOL installation which can be found by > python, the launcher will use that one! (this could be improved I guess). > > Cheers, > Thomas > |
From: Jason V. <jas...@sc...> - 2011-06-16 14:42:19
|
Hi Zhijian, I recompiled from SVN to test this and the message is no longer emitted (with default feedback settings). If you have raised the internal feedback of object molecule to "blather" then you'll see this message. Please try pulling again (ensuring you have commit 3955) and rebuilding. I also suggest cleaning the last version before installing. Cheers, -- Jason On Thu, Jun 16, 2011 at 10:24 AM, zjxu <zj...@ma...> wrote: > Dear Jason, > I am afraid the change did not work for me. Is there anything wrong in my > rebuild process? > (1) I download the source code with the command: svn co > https://pymol.svn.sourceforge.net/svnroot/pymol pymol > (2) go to pymol/trunk/pymol, and see the ChangeLog: 2011-06-16 Jason > Vertrees <Jas...@sc...> > > * suppress guess valences warning message to Blather > (3) In pymol/trunk/pymol: > python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ > python setup2.py install > ./pymol > However, when I load a pdb, the warning comes again. "pymol -rkqc script.py" > complains again. > > Best Regards, > Zhijian Xu > > zjxu wrote: >> >> Dear Jason, >> Thanks very much for the prompt reply. >> Yes, I compiled pymol by hand from source under Linux and I will rebuild >> it. >> >> Best Regards, >> Zhijian Xu >> >> Jason Vertrees wrote: >> >>> >>> Hi Zhijian, >>> >>> In PyMOL v1.4 and PyMOL v1.4.1 this message will be emitted. We have >>> changed this warning message for later versions to be released in a >>> few months' time. If you're using the open-source code, then a >>> rebuild from source should fix this for you. I just pushed the change >>> to the open-source project a few moments ago. >>> >>> Cheers, >>> >>> -- Jason >>> >>> >>> >>> On Thu, Jun 16, 2011 at 8:52 AM, zjxu <zj...@ma...> wrote: >>> >>>> >>>> Dear everyone, >>>> when I run a script in pymol1.4.1 on the command line: pymol -rqkc >>>> script.py. >>>> Then a lot of messages "ObjectMoleculeGuessValences(1,1): Unreasonable >>>> connectivity in heteroatom, >>>> unsuccessful in guessing valences." will be printed out on the screen >>>> in addition to the script results. >>>> It is somewhat annoying. Is there any option to turn this off? >>>> Pymol1.3 works without the above complain messages. >>>> Thanks in advance. >>>> >>>> Zhijian Xu >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> EditLive Enterprise is the world's most technically advanced content >>>> authoring tool. Experience the power of Track Changes, Inline Image >>>> Editing and ensure content is compliant with Accessibility Checking. >>>> http://p.sf.net/sfu/ephox-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... >>>> >>>> >>> >>> >> >> >> >> ------------------------------------------------------------------------------ >> EditLive Enterprise is the world's most technically advanced content >> authoring tool. Experience the power of Track Changes, Inline Image >> Editing and ensure content is compliant with Accessibility Checking. >> http://p.sf.net/sfu/ephox-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 PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: zjxu <zj...@ma...> - 2011-06-16 15:08:52
|
Dear Jason, I will try again. Thanks for the advice. Best Regards, Zhijian Xu Jason Vertrees wrote: > Hi Zhijian, > > I recompiled from SVN to test this and the message is no longer > emitted (with default feedback settings). If you have raised the > internal feedback of object molecule to "blather" then you'll see this > message. > > Please try pulling again (ensuring you have commit 3955) and > rebuilding. I also suggest cleaning the last version before > installing. > > Cheers, > > -- Jason > > On Thu, Jun 16, 2011 at 10:24 AM, zjxu <zj...@ma...> wrote: > >> Dear Jason, >> I am afraid the change did not work for me. Is there anything wrong in my >> rebuild process? >> (1) I download the source code with the command: svn co >> https://pymol.svn.sourceforge.net/svnroot/pymol pymol >> (2) go to pymol/trunk/pymol, and see the ChangeLog: 2011-06-16 Jason >> Vertrees <Jas...@sc...> >> >> * suppress guess valences warning message to Blather >> (3) In pymol/trunk/pymol: >> python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ >> python setup2.py install >> ./pymol >> However, when I load a pdb, the warning comes again. "pymol -rkqc script.py" >> complains again. >> >> Best Regards, >> Zhijian Xu >> >> zjxu wrote: >> >>> Dear Jason, >>> Thanks very much for the prompt reply. >>> Yes, I compiled pymol by hand from source under Linux and I will rebuild >>> it. >>> >>> Best Regards, >>> Zhijian Xu >>> >>> Jason Vertrees wrote: >>> >>> >>>> Hi Zhijian, >>>> >>>> In PyMOL v1.4 and PyMOL v1.4.1 this message will be emitted. We have >>>> changed this warning message for later versions to be released in a >>>> few months' time. If you're using the open-source code, then a >>>> rebuild from source should fix this for you. I just pushed the change >>>> to the open-source project a few moments ago. >>>> >>>> Cheers, >>>> >>>> -- Jason >>>> >>>> >>>> >>>> On Thu, Jun 16, 2011 at 8:52 AM, zjxu <zj...@ma...> wrote: >>>> >>>> >>>>> Dear everyone, >>>>> when I run a script in pymol1.4.1 on the command line: pymol -rqkc >>>>> script.py. >>>>> Then a lot of messages "ObjectMoleculeGuessValences(1,1): Unreasonable >>>>> connectivity in heteroatom, >>>>> unsuccessful in guessing valences." will be printed out on the screen >>>>> in addition to the script results. >>>>> It is somewhat annoying. Is there any option to turn this off? >>>>> Pymol1.3 works without the above complain messages. >>>>> Thanks in advance. >>>>> >>>>> Zhijian Xu >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> EditLive Enterprise is the world's most technically advanced content >>>>> authoring tool. Experience the power of Track Changes, Inline Image >>>>> Editing and ensure content is compliant with Accessibility Checking. >>>>> http://p.sf.net/sfu/ephox-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... >>>>> >>>>> >>>>> >>>> >>> >>> ------------------------------------------------------------------------------ >>> EditLive Enterprise is the world's most technically advanced content >>> authoring tool. Experience the power of Track Changes, Inline Image >>> Editing and ensure content is compliant with Accessibility Checking. >>> http://p.sf.net/sfu/ephox-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... >>> >>> >>> >>> >> > > > > |