From: NICHOLAS F. <nic...@jh...> - 2003-07-08 18:26:56
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> 4- Is there any chance you will be able to > include non-continuous selections ie > select (resi 10-20,30-40) rather than just > 10-20 and ignore residues 30-40? > Jules, It's a little more cumbersome, but one way to do the above selection would be: select resi 10-20 or resi 30-40 select chain A and (resi 10-20 or resi 30-40) It's not quite as convenient, but it gets the job done. Regards, Nick -- Nicholas Fitzkee nic...@jh... "I would like to share with you what makes me complete. I don't claim to have found the Truth, but I know It has found me. The only thing that isn't meaningless to me is Jesus Christ and and way he set me free. This is all that I have. This is all that I am." -- Sara Groves, "Conversations" |
From: Warren L. D. <wa...@de...> - 2003-07-08 23:28:04
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> 1- calculation of surface potentials- will this be coming soon? Creation of a Possion-Boltzman solver is a bit of work, so this will not happen very soon -- probably not until we accumulate enough sponsorship to contract with someone to perform the task. But perhaps someone might volunteer to write an open-source Python PB module in the meantime? [sounds like a good summer project for a graduate student in computational chemistry : )] In the meantime, I recommend using Grasp to calculate the potential, saving the potential as a ".phi" file, and then loading the potential into PyMOL for visualization. Delphi should work too in theory, but we're currently working to resolve a few problems with the approach... > 2- Are you thinking of including any kind of sequence viewer and > sequence alignment tools to tie in with the fitting - as seen with > swissPDB? This would be verh high on my wishlist. It is high on my list as well. > 3- Will you be including any more NMR biased features like a quick > fitting and RMSD calculation for ensembles of structures? This is currently possible using "intra_fit" if the ensemble is loaded as a single object. Between objects, you can do pair-wise fits using "fit" or "align", but that gets tedious with a lot of structures. The sequence viewer will hopefully make multi-object fitting easier. > 4- Is there any chance you will be able to include non-continuous > selections ie select (resi 10-20,30-40) rather than just 10-20 and > ignore residues 30-40? This is already possible using the selection macros: 10-20,30-40/ which is equivalent to resi 10-20 or resi 30-40 Please see the new "Command Syntax and Atom Selections" chapter in the User's Manual for more information on selections. http://pymol.sourceforge.net/newman/user/S0220commands.html#7 Cheers, Warren |
From: Anthony D. <A....@us...> - 2003-07-09 00:23:05
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Can pymol, or will it in the near future, work with anisotropic b-factors and display thermal ellipsoids? Alternatively, can pymol do anything with the output of rastep? Anthony ---------------------------------------------------------------------- Anthony Duff Postdoctoral Fellow School of Molecular and Microbial Biosciences Biochemistry Building, G08 University of Sydney, NSW 2006 Australia Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 ---------------------------------------------------------------------- |
From: <pm...@ua...> - 2003-07-09 12:54:04
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Quoting "Warren L. DeLano" <wa...@de...>: > > 1- calculation of surface potentials- will this be coming soon? > > Creation of a Possion-Boltzman solver is a bit of work, so this will not > happen very soon -- probably not until we accumulate enough sponsorship > to contract with someone to perform the task. But perhaps someone might > volunteer to write an open-source Python PB module in the meantime? > [sounds like a good summer project for a graduate student in > computational chemistry : )] > > In the meantime, I recommend using Grasp to calculate the potential, > saving the potential as a ".phi" file, and then loading the potential > into PyMOL for visualization. Delphi should work too in theory, but > we're currently working to resolve a few problems with the approach... > Another possibility is to use the "potential" program in Don Bashford's MEAD package. It produces a .phi potential file that should work in Pymol with a small amount of tweaking (it works with Dino). Cheers, Paulo --- Paulo Martel Dept. of Chemistry and Biochemistry Universidade do Algarve Campus de Gambelas, 8000 Faro PORTUGAL |
From: Marc S. <mar...@gm...> - 2003-07-09 07:30:15
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 | Message: 4 From: "Warren L. DeLano" <wa...@de...> |>> 1- calculation of surface potentials- will this be coming soon? | | Creation of a Possion-Boltzman solver is a bit of work, so this will | not happen very soon -- probably not until we accumulate enough | sponsorship to contract with someone to perform the task. But | perhaps someone might volunteer to write an open-source Python PB | module in the meantime? [sounds like a good summer project for a | graduate student in computational chemistry : )] | | In the meantime, I recommend using Grasp to calculate the potential, Downside: You need an SGI to do that (not everyone has). And GRASP is not free in any way. Is there a possibility to utilize APBS (which is GPLed at least) (see http://agave.wustl.edu/apbs/)?? It should run under Linux and other unix-flavours. I haven't used it really, but I think it should do the thing (don't know about the speed etc.). The question is, wether one could convert the output to something, Pymol can read... | saving the potential as a ".phi" file, and then loading the potential | into PyMOL for visualization. Delphi should work too in theory, but | we're currently working to resolve a few problems with the | approach... - -- Bye, Marc Saric http://www.marcsaric.de -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQE/C8RuvKxJUF29wRIRAmM1AJ9r2tZEHISCg72pqqhE2cnwXgahRACgyrQc lAXSEBi9KR0IXZ5p0BVTzng= =IeYc -----END PGP SIGNATURE----- |