if just add strings in pymol's cmd the "Super version" of the script works fine so the problem is indeed in MAC :)
2017-07-18 20:53 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: > 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 probably because of my MAC Pymol which is v 1.74 mb outdated, no?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
