[PyMOL] Structure and map comparison like Phenix
Dear PyMOL users... Have you tried to compare several structures and maps? I am talking about something like this ( https://www.phenix-online.org/documentation/reference/structure_comparison.html ) Are there any good pymol scripts that can make this easier? Although the table phenix outputs looks very nice I am happy with just aligning the pdbs (that's easy) and the maps* (that I do not know how to do). map* i.e. in ccp4 or mtz format. Ps. I would normally use the phenix program in the url above, but a bug is standing in the way. -- 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] PyMOL Open-Source Fellowship - Call for Applications
Greetings, We are excited to announce that the Warren L. DeLano Memorial PyMOL Open-Source Fellowship program is now accepting applications for the 2018--2019 term. The Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community to develop free resources to help scientific progress and the community as a whole. Details and application instructions can be found on https://pymol.org/fellowship The application deadline is August 26, 2018. We look forward to your submissions! Cheers, The PyMOL Team at Schrödinger -- 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] SMILES pattern recognition ability of PyMOL
Dear PyMOL Users,
I am using Open source PyMOL 2.1 installed on Windows 10 (Python 3.6). I
found a very interesting ability of PyMOL which is related to SMILES
pattern matching. With the help of following code, I am able to get count
of matches for a specified SMILES pattern. For example, I used
"C1*CC*CC*N1" pattern to get number of Pyridine rings (actually the pattern
refers to "six membered aromatic ring containing Nitrogen"). Now, I want to
develop a method to use this pattern recognition ability of PyMOL to select
the atoms which matches the given SMILES pattern.
from chempy import champ
from chempy.champ import Champ
ch=Champ()
model = cmd.get_model('all')
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("C1*CC*CC*N1")
abc = ch.match_1v1_n(assn_pat,model_pat,1,2)
xyy = ch.pattern_get_string(model_pat)
print (abc)
Thanks in advance.
Cheers
Vijay
--
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/
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[PyMOL] Virtual screening with Autodock Vina
Hi everyone, I am trying to perform a virtual screening using autodock vina. However, in this particular case I am using different proteins and one single substrate. I don't know if this can be done automatically with a script. I've found some scripts for one protein and several substrates witch seems to be easier. I have a library of hundreds of proteins and doing this manually is a bit tiresome and time consuming. Best regards, Enrique Ordaz -- 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] AutoDock plugin error
Hi, I thank you all for your answers and all the help provided. I will try to solve the problem with all the info I got and let you know the results. Best regards, Enrique 2018-06-13 10:20 GMT-05:00 Thomas Holder : > Hi all, > > I made a pull request to Pymol-script-repo where oldnumeric is replaced > with numpy in the bundled ADT copy. Anyone willing to review and test this? > > https://github.com/Pymol-Scripts/Pymol-script-repo/pull/98 > > Cheers, > Thomas > > > On Jun 13, 2018, at 11:24 AM, J.R. W wrote: > > > > Enrique, > > > > I don’t know a lot about AutoDock, but I do know a lot about python. > That error comes from using a new versions of numpy (1.14) that does not > have old numeric with it anymore (deprecated in 1.9). > > > > You can do a few things. Run the script within pymol which uses a > earlier release of numpy. rOr you could downgrade your numpy to 1.8 by using > > > > Pip install ‘numpy==1.8’ —force-reinstall > > > > > > But I’d recommend you do that in an environment. This is the perfect > time for virtual environments > > > > https://realpython.com/python-virtual-environments-a-primer/ > > > > > > > >> On Jun 12, 2018, at 2:36 PM, Enrique Ordaz > wrote: > >> > >> Dear everyone, > >> I have recently installed the open-source Pymol 1.7.x on Ubuntu 16.04 > >> sudo-apt-get install pymol > >> > >> I then added the Pymol-script-repo which includes the Autodock/Vina > plugin and ADT. This has worked well for me in the past. However on this > new installation I keep getting the following error: > >> > >> Batch: /home/enrique/Pymol-script-repo/modules/ADT/ > AutoDockTools/Utilities24/prepare_receptor4.py -r > /home/enrique/pymol/receptor.1crl.pdb -o > /home/enrique/pymol/receptor.1crl.pdbqt > -A checkhydrogens > >> Traceback (most recent call last): > >> File "/home/enrique/Pymol-script-repo/modules/ADT/ > AutoDockTools/Utilities24/prepare_receptor4.py", line 10, in > >> import MolKit.molecule > >> File "/home/enrique/Pymol-script-repo/modules/ADT/MolKit/molecule.py", > line 25, in > >> from mglutil.util import misc > >> File "/home/enrique/Pymol-script-repo/modules/ADT/mglutil/util/misc.py", > line 19, in > >> import numpy.oldnumeric as Numeric > >> ImportError: No module named oldnumeric > >> > >> Hope someone can help me or point me in the right direction. > >> > >> Best regards, > >> Enrique Ordaz > > -- > 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
