Re: [PyMOL] rejected atoms during alignment
the problem in this case is to recognize the rejected atoms by eye, if you align about 400 c-alphas with average RMSDs of 0.2A. a printable list would be more helpful. but i guess this is not possible. but thanks a lot for your answer. On Thursday 03 August 2006 17:25, you wrote: This is not a great answer, but do you know about the object parameter for the align command? I often type something like align struct1, struct2, object=alignment and then just look at which things were included/excluded. -michael On 8/3/06, Marc Bruning brun...@mpghdb.desy.de wrote: hello, is there any way to find out which atoms are discarded during the refinement cycles of the align command? regards, marc - 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] rejected atoms during alignment
hello, is there any way to find out which atoms are discarded during the refinement cycles of the align command? regards, marc
[PyMOL] gui/viewer position
hello, is it possible to define the gui and viewer positions on startup separately? thanks, marc
Re: [PyMOL] automated H-bond computation visualization in pyMOL?
hello, is this feature accessible from the command line as well? cheers, marc On Monday 17 October 2005 22:16, Warren DeLano wrote: Michael d/l a recent build http://delsci.com/beta and use the find-polar contacts option under the objects Action A menu in the viewer window. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Michael Weber Sent: Monday, October 17, 2005 5:03 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] automated H-bond computation visualization in pyMOL? Hello everybody, I am new to PyMOL and I have a short question: In pyMOL - is it possible to automatically compute and visualize H-bonds in .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe there is a pyMOL script for this purpose? I need such a function for my work with catalytically active RNA molecules (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice if someone could help me with this problem... All the best thanks in advance, Michael. --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] alignment question
hello, is there any possibility to get a list of the pairs of atoms that are matched using the align command? cheers, marc
Re: [PyMOL] select all aminoacids and not ligand
in case your ligand has a different chain id than your protein, you could use that to distinguish. On Tuesday 12 July 2005 11:59, Andrea Spitaleri wrote: Hi all is there any shortcut to select all aminoacid in a complex and not the ligand? something like select my, all and not ligand where I don't know the resn of the ligand but in my script I should be able to discern between aminoacids (ALA,VAL, etc...) and not. thanks in advance Regards andrea --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- ..--.:..:
[PyMOL] display variables
dear list, is it possible to distribute the pymol gui and the viewer between different display variables, say the gui to display:0.0 and the viewer to display:0.1? regards, marc bruning
