The link wasn't a direct link to the fixed setup.py file. The direct link is: https://raw.githubusercontent.com/speleo3/pymol-psico/master/setup.py
MacPyMOL 1.7.4 is recent enough for this exercise. However, your MacPyMOL installation and your Anaconda3 Python are unrelated, so installing PSICO with Anaconda won't make it work with MacPyMOL. The simplest approach to install PSICO with MacPyMOL is to copy the "psico" directory here: /Applications/MacPyMOL.app/Contents/pymol/modules/ Cheers, Thomas > On Jul 18, 2017, at 2:53 PM, James Starlight <jmsstarli...@gmail.com> wrote: > > There were some errors in the executing pymol script with your commands using > @ script.pml > or > run script.pml > > probably because of my MAC Pymol which is v 1.74 mb outdated, no? > > BTW on the same MAC I just have tried to install updated setup.py and > it was the following error: > > Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py > File "setup.py", line 7 > <!DOCTYPE html> > ^ > SyntaxError: invalid syntax > > 2017-07-18 19:52 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: >> With super instead of tmalign: >> >> loadall *.pdb >> extra_fit *, reference, method=super, object=aln >> remove not (byres aln) >> >> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now: >> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af >> >> Cheers, >> Thomas >> >>> On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote: >>> >>> Hi Thomas, >>> >>> could you also send the same script but just with the Super command >>> for the superimposition without PSICO? >>> >>> it's strange I have a problems of PSICO installation on MAC with python 3 >>> >>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >>> Type "help", "copyright", "credits" or "license" for more information. >>>>>> >>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t >>> README psico setup.py >>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py >>> File "setup.py", line 10 >>> print 'Warning: could not import version' >>> ^ >>> >>> 2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: >>>> Hi Thomas, >>>> >>>> could you also send the same script but just with the Super command >>>> for the superimposition without PSICO? >>>> >>>> it's strange I have a problems of PSICO installation on MAC with python 3 >>>> >>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >>>> Type "help", "copyright", "credits" or "license" for more information. >>>>>>> >>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t >>>> README psico setup.py >>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py >>>> File "setup.py", line 10 >>>> print 'Warning: could not import version' >>>> ^ >>>> SyntaxError: Missing parentheses in call to 'print' >>>> >>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: >>>>> Hi Gleb, >>>>> >>>>> If you have PSICO installed (which provides a TMalign wrapper), then this >>>>> script should be sufficient: >>>>> >>>>> loadall *.pdb >>>>> import psico.fitting >>>>> extra_fit *, reference, method=tmalign, object=aln >>>>> remove not (byres aln) >>>>> >>>>> https://pymolwiki.org/index.php/Psico >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> >>>>>> wrote: >>>>>> >>>>>> Dear Pymol Users! >>>>>> >>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor >>>>>> reference.pdb (it consist of only one GPCR monomer - seven >>>>>> transmbembrane scaffold). >>>>>> >>>>>> I need to write a simple script which will do the following things: >>>>>> >>>>>> 1 - allign (in loop) each structure against reference.pdb using >>>>>> "super" or "TMalign" (is better!) >>>>>> >>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions >>>>>> (assuming that each pdb has several chains, some insertions like >>>>>> lyzocyme which were not aligned against reference), thus keeping only >>>>>> seven-transmembrane scaffold present in reference.pdb. >>>>>> >>>>>> I thanks so much for the help! >>>>>> >>>>>> Gleb -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
