[PyMOL] hydrogen_add problem
Hello everybody, I'm currently working on a java project in which, after loading a pdb-file, I need to add Hydrogens to the molecules. Since Pymol has an implemented method for this problem, I'd be interested in the algorithm used, so I can reimplement it in java. Does anybody know if there is a publication, where I can find it? Another approach I am following is the usage of the CDK package, but I'm not really sure how to apply it to my problem and how good the method works. I'd be thankful for any help I can get ;). greetings, Danrik -- Ein Herz für Kinder - Ihre Spende hilft! Aktion: www.deutschlandsegelt.de Unser Dankeschön: Ihr Name auf dem Segel der 1. deutschen America's Cup-Yacht!
Re: [PyMOL] hydrogen_add problem
You should take a look at the program Reduce from the Richardson lab at Duke, it adds protons and is written in C++. It will take a pdb and without requiring modification or formating add protons to it. Versions exist for Linux, Windows, MacOS X, Irix, and Sun-SPARC, and the source code is available as well. It can be used as a plug-in program, just call out to it with whatever options are required, then get back the protenated pdb. Information and references (including algorithms published in JMB) at http://kinemage.biochem.duke.edu/software/reduce.php Note: not a member of the Richardson lab, but a (program using) collaborator. S. Endo-Streeter On Wednesday 06 December 2006 08:55, d.gottst...@gmx.de wrote: Hello everybody, I'm currently working on a java project in which, after loading a pdb-file, I need to add Hydrogens to the molecules. Since Pymol has an implemented method for this problem, I'd be interested in the algorithm used, so I can reimplement it in java. Does anybody know if there is a publication, where I can find it? Another approach I am following is the usage of the CDK package, but I'm not really sure how to apply it to my problem and how good the method works. I'd be thankful for any help I can get ;). greetings, Danrik -- __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu
Re: [PyMOL] hydrogen_add problem
Hi, I also would vote for using reduce, since it is very good. If you have to do it in pure java (ie: not calling reduce from java somehow) then cdk would also be a good choice. A quick scan through the api gives: org.openscience.cdk.tools.HydrogenAdder which Provides methods for adding missing hydrogen atoms. - seems perfect :) gilleain torrance On 12/6/06, Stuart Endo-Streeter stuart.endostree...@duke.edu wrote: You should take a look at the program Reduce from the Richardson lab at Duke, it adds protons and is written in C++. It will take a pdb and without requiring modification or formating add protons to it. Versions exist for Linux, Windows, MacOS X, Irix, and Sun-SPARC, and the source code is available as well. It can be used as a plug-in program, just call out to it with whatever options are required, then get back the protenated pdb. Information and references (including algorithms published in JMB) at http://kinemage.biochem.duke.edu/software/reduce.php Note: not a member of the Richardson lab, but a (program using) collaborator. S. Endo-Streeter On Wednesday 06 December 2006 08:55, d.gottst...@gmx.de wrote: Hello everybody, I'm currently working on a java project in which, after loading a pdb-file, I need to add Hydrogens to the molecules. Since Pymol has an implemented method for this problem, I'd be interested in the algorithm used, so I can reimplement it in java. Does anybody know if there is a publication, where I can find it? Another approach I am following is the usage of the CDK package, but I'm not really sure how to apply it to my problem and how good the method works. I'd be thankful for any help I can get ;). greetings, Danrik -- __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] ImportError
Dear developers, just to inform, after some reinitializations of Pymol 0.99rc6 (pre-compiled) in a same session, I have got the message bellow (restarted the program and it was ok again). (I don't know if its due to my Linux installation or Pymol). Cheers, Ricardo Error: 3 ImportError Exception in Tk callback Function: function lambda at 0xb6b97a04 (type: type 'function') Args: () Traceback (innermost last): File /home/aparicio/test_pymol2/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, line 1747, in __call__ None File /home/aparicio/test_pymol2/pymol/modules/pmg_tk/skins/normal/__init__.py, line 1520, in lambda None File /home/aparicio/test_pymol2/pymol/modules/pmg_tk/SetEditor.py, line 78, in __init__ None File /home/aparicio/test_pymol2/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwLoader.py, line 145, in __getattr__ None File /home/aparicio/test_pymol2/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwLoader.py, line 71, in _getmodule None ImportError: No module named PmwSelectionDialog
