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