[PyMOL] Handling of scene specific global settings?
Hi, with the current refactoring of the scene code was there any consideration given to the handling of scene specific global settings? For instance "cartoon putty" vs. "cartoon automatic" or settings like "sphere_scale" are only applied once on a global scope and carry over to all scenes, even though in my script they have been defined individually for different scenes. Right now I am using 1.7.3, but was wondering if anything has changed in 1.7.6 in that regard? The issue is not new, but it would be nice if there would be a feature like this implemented. Cheers, Carsten -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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] regarding theseus wrapper
Hi Priyan, I updated the wrapper, it now supports THESEUS 3.x: https://github.com/speleo3/pymol-psico Cheers, Thomas On 15 May 2015, at 07:26, Thomas Holder wrote: > Hi Priyan, > > the wrapper fails because THESEUS 3.0.0 changed the output. I suggest to use > THESEUS 2.x until I (or someone else) have updated the wrapper to handle the > new output files. > > Link to THESEUS 2.x source that works for me: > http://www.theseus3d.org/src/theseus_2.0.6.tar.gz > > Or ask the theseus author for a binary. > > Cheers, > Thomas > > On 07 May 2015, at 23:05, ccp4 pymol wrote: > >> Dear pymol-users >> >> There is some trouble I end up with while using theseus from psico in pymol. >> I am not sure what is causing this. Can anyone help me fix this one. The log >> I get when executing theseus is given below. >> >> thank you in advance, >> >> Best Regards >> Priyan >> >> BEGIN THESEUS 3.0.0 > >> I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=I >> ITHESEUS: Maximum likelihood multiple superpositioning >> I >> I=-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===I >>Reading pdb file ... >>Successfully read 2 models and/or structures >>Selecting coordinates for superposition ... >>Calculating superposition transformations ... >>Aborting at iteration 2 >> Traceback (most recent call last): >> File "/media/XTAL/pymol/modules/pymol/parser.py", line 256, in parse >>self.result=apply(layer.kw[0],layer.args,layer.kw_args) >> File "/media/XTAL/pymol/modules/psico/fitting.py", line 712, in theseus >>translations, rotations = _run_theseus(args, tempdir, preserve, quiet) >> File "/media/XTAL/pymol/modules/psico/fitting.py", line 648, in _run_theseus >>handle = open(os.path.join(tempdir, 'theseus_transf2.txt')) >> IOError: [Errno 2] No such file or directory: >> '/tmp/tmpwXC24Y/theseus_transf2.txt' -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ 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] regarding theseus wrapper
Hi Priyan, the wrapper fails because THESEUS 3.0.0 changed the output. I suggest to use THESEUS 2.x until I (or someone else) have updated the wrapper to handle the new output files. Link to THESEUS 2.x source that works for me: http://www.theseus3d.org/src/theseus_2.0.6.tar.gz Or ask the theseus author for a binary. Cheers, Thomas On 07 May 2015, at 23:05, ccp4 pymol wrote: > Dear pymol-users > > There is some trouble I end up with while using theseus from psico in pymol. > I am not sure what is causing this. Can anyone help me fix this one. The log > I get when executing theseus is given below. > > thank you in advance, > > Best Regards > Priyan > > BEGIN THESEUS 3.0.0 > > I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=I > ITHESEUS: Maximum likelihood multiple superpositioning > I > I=-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===I > Reading pdb file ... > Successfully read 2 models and/or structures > Selecting coordinates for superposition ... > Calculating superposition transformations ... > Aborting at iteration 2 > Traceback (most recent call last): > File "/media/XTAL/pymol/modules/pymol/parser.py", line 256, in parse > self.result=apply(layer.kw[0],layer.args,layer.kw_args) > File "/media/XTAL/pymol/modules/psico/fitting.py", line 712, in theseus > translations, rotations = _run_theseus(args, tempdir, preserve, quiet) > File "/media/XTAL/pymol/modules/psico/fitting.py", line 648, in _run_theseus > handle = open(os.path.join(tempdir, 'theseus_transf2.txt')) > IOError: [Errno 2] No such file or directory: > '/tmp/tmpwXC24Y/theseus_transf2.txt' -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ 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
