Thread: [Apbs-users] electrostatic potential near an aminoacid
Biomolecular electrostatics software
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From: Davide C. <dav...@if...> - 2008-08-12 11:27:07
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Dear users, I'm pretty new to this kind of problems, so forgive me in advance if I ask the wrong questions... I use apbs to calculate the potential surface over the entire protein, and I only have a clue about the potential in certain protein regions but I would like to know the exact value (or, at least, a range). Is there a way with apbs+pymol to know the exact potential value within a given radius near to specified residues? Moreover, what is the format of .dx files? I believe I can somehow look at those to have my value back... Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: dav...@if... */ |
From: Nathan B. <nat...@ma...> - 2008-08-13 00:46:29
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Hello -- It sounds like you could use the multivalue tool provided with APBS (tools/mesh/multivalue) for this purpose. This will return values of the potential at user-specified points. The format of the OpenDX files is described in the User Guide: http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format Thanks, Nathan On Aug 12, 2008, at 6:27 AM, Davide Cittaro wrote: > Dear users, > I'm pretty new to this kind of problems, so forgive me in advance if > I ask the wrong questions... > I use apbs to calculate the potential surface over the entire > protein, and I only have a clue about the potential in certain > protein regions but I would like to know the exact value (or, at > least, a range). Is there a way with apbs+pymol to know the exact > potential value within a given radius near to specified residues? > Moreover, what is the format of .dx files? I believe I can somehow > look at those to have my value back... > > Thanks > > d > > > /* > Davide Cittaro > > Cogentech - Consortium for Genomic Technologies > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303007 > e-mail: dav...@if... > */ > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Davide C. <dav...@if...> - 2008-08-13 07:51:30
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Hi On Aug 13, 2008, at 2:46 AM, Nathan Baker wrote: > > It sounds like you could use the multivalue tool provided with APBS > (tools/mesh/multivalue) for this purpose. This will return values > of the potential at user-specified points. > Great thanks! I'll try it! d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: dav...@if... */ |