Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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 > -- 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
Re: [PyMOL] How to merge molecules in Pymol?
Hi Carsten, > Is there an (un)documented way of merging multiple molecular objects in > Pymol into one molecule, which then can be written in a nicely formatted PDB > file? I cobbled something cludgy together with ‘multisave’ and a couple > read-sort-save cycles, but this is ugly and probably quite fragile. An API > function might be much more robust. Is there a provision like this in > ChemPy? I’ve already taken care of adjusting each molecule to be unique with > respect to chain IDs and IDs, so that would not be an issue. It's documented: * help create * http://www.pymolwiki.org/index.php/Create Create can be used to create a single single-state object or a single multi-state object. The former will just 'do what you say' but may create biologically unrealistic molecules (it just combines the objects). The latter is better as it saves to biologically realistic multi-state pdbs. Try these examples: # method 1 # create a single state (possibly biologically infeasible) molecule # from two objects frag ala frag cys save test.pdb, ala or cys Now load "test.pdb". # method 2 # create a single multi-state object from two molecules frag ala frag cys create test, ala, 1, 1 create test, cys, 1, 2 save test.pdb, test, state=0 Cheers, -- Jason On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS] wrote: > Hi, > > Is there an (un)documented way of merging multiple molecular objects in > Pymol into one molecule, which then can be written in a nicely formatted PDB > file? I cobbled something cludgy together with ‘multisave’ and a couple > read-sort-save cycles, but this is ugly and probably quite fragile. An API > function might be much more robust. Is there a provision like this in > ChemPy? I’ve already taken care of adjusting each molecule to be unique with > respect to chain IDs and IDs, so that would not be an issue. > > Any pointers would be appreciated. > > Cheers, > > Carsten > > -- > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] How to merge molecules in Pymol?
Hi, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with 'multisave' and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An API function might be much more robust. Is there a provision like this in ChemPy? I've already taken care of adjusting each molecule to be unique with respect to chain IDs and IDs, so that would not be an issue. Any pointers would be appreciated. Cheers, Carsten -- 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
Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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 -- 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
Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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 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 >> >> * 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 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
Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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 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 > > * 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 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 >> >> >> > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] Flickering
Dear PyMOL community, My PyMOL application is exhibiting flickering whenever I launch it. I running on a Intel Core 2 duo on OS X 10.7. This happens without loading any PDB structures, simply by launching the program. Has this been encountered before? Spyros -- 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
Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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 * 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 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
Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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 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
Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
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
