[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

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

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

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

[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

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

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

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

[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

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

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