Re: [PyMOL] Retain order for select segment and write trajectory
Hi Kelly, With retain_order=1, PyMOL will sort by rank, which is the order of time of loading the structure. By setting all rank values to the same value, you'll get segi/chain/resi sorting. So to preserve rank based sorting only for non-solvent, you can do this: set retain_order alter solvent, rank=-1 sort This will sort solvent to the beginning. To put it to the end, pick a number which is beyond the atom count. set retain_order alter solvent, rank= sort The atom ID is never used for sorting. But you could incorporate it in the ranks: set retain_order alter solvent, rank= + ID sort Cheers, Thomas > On Jul 18, 2017, at 2:09 PM, Kelly Tran wrote: > > Hi, > > I'm using PSICO to write a DCD. Is it possible to retain the original order > for one segment (protein) while sorting by atom ID for another segment > (water). > > Thank you, > > Kelly -- 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
Re: [PyMOL] A structural superimposition and further post-processing
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 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 probably because of my MAC Pymol which is v 1.74 mb outdated, no?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 > >^ > SyntaxError: invalid syntax > > 2017-07-18 19:52 GMT+02:00 Thomas Holder : >> 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 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 >>> READMEpsicosetup.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 : 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 READMEpsicosetup.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 : > 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 >> 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
Re: [PyMOL] A structural superimposition and further post-processing
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 : > 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 > > ^ > SyntaxError: invalid syntax > > 2017-07-18 19:52 GMT+02:00 Thomas Holder : >> 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 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 >>> READMEpsicosetup.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 : 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 READMEpsicosetup.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 : > 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 >> 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
Re: [PyMOL] A structural superimposition and further post-processing
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 ^ SyntaxError: invalid syntax 2017-07-18 19:52 GMT+02:00 Thomas Holder : > 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 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 >> READMEpsicosetup.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 : >>> 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 >>> READMEpsicosetup.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 : 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 > 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
[PyMOL] Retain order for select segment and write trajectory
Hi, I'm using PSICO to write a DCD. Is it possible to retain the original order for one segment (protein) while sorting by atom ID for another segment (water). Thank you, Kelly -- 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
Re: [PyMOL] A structural superimposition and further post-processing
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 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 > READMEpsicosetup.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 : >> 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 >> READMEpsicosetup.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 : >>> 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 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
Re: [PyMOL] A structural superimposition and further post-processing
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 READMEpsicosetup.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 : > 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 > READMEpsicosetup.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 : >> 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 >>> 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
Re: [PyMOL] A structural superimposition and further post-processing
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 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
[PyMOL] A structural superimposition and further post-processing
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 -- 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
