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 <[email protected]> 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 <[email protected]> >> >> * 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 <[email protected]> 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 ([email protected]) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/[email protected] >>>>> >>>>> >>>>> >>>> >>> >>> ------------------------------------------------------------------------------ >>> 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 ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >>> >>> >>> >> > > > > ------------------------------------------------------------------------------ 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 ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
