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
