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 <jason.vertr...@schrodinger.com>
* 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 <z...@mail.shcnc.ac.cn> 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 (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 >>> >>> >>> >> >> >> > > > ------------------------------------------------------------------------------ > 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 (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 > > > ------------------------------------------------------------------------------ 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 (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
