From: Heinz-Uwe H. <uwe...@tg...> - 2005-05-03 17:03:09
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Hi, assume you have a protein structure (P1) and a second protein sequence (S1) without structure. Both sequences align with about 50% sequence identity over a large portion of both sequences without gaps (Smith+Waterman). Is there a way to automatically exchange residues from P1 against the respective residues in S1 (maybe using a script that exploits the mutate wizzard residue by residue ?) and do a final bond relaxation / sidechain orientation / H-bond-length correction ? Yes, I know, this is more than visualizing ... Best regards Uwe Hobohm |
From: Scott C. <cl...@uc...> - 2005-05-03 18:17:40
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Hi Uwe, try Modeller: http://salilab.org/modeller/ Ciao, Scott On May 3, 2005, at 10:02 AM, Heinz-Uwe Hobohm wrote: > Hi, > > assume you have a protein structure (P1) and a second protein > sequence (S1) without structure. Both sequences align with about > 50% sequence identity over a large portion of both sequences > without gaps (Smith+Waterman). > > Is there a way to automatically exchange residues from P1 against > the respective residues in S1 (maybe using a script that exploits > the mutate wizzard residue by residue ?) and do a final bond > relaxation / sidechain orientation / H-bond-length correction ? > > Yes, I know, this is more than visualizing ... > > Best regards > Uwe Hobohm > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. > Get your fingers limbered up and give it your best shot. 4 great > events, 4 > opportunities to win big! Highest score wins.NEC IT Guy Games. Play to > win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
From: Heinz-Uwe H. <uwe...@tg...> - 2005-05-09 14:48:36
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Thanks for the replies on my "How to spoil PyMol for modelling" request. Despite Peitzsch's SwissModel (very convenient) and Sali's Modeller (less convenient but perhaps more precise ?) I would like to know, for educational purposes, whether PyMol could do reasonably well also. To be more precise; assume you apply a script like cmd.edit("(1NOT`3)",pkresi=1) wizard mutagenesis refresh_wizard cmd.get_wizard().set_mode("ALA") cmd.get_wizard().apply() cmd.set_wizard() residue by residue according to the alignment, which further (scriptable !) refinement steps are available in PyMol ? |
From: Warren D. <wa...@de...> - 2005-05-09 17:35:22
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Heinz-Uwe, Not much. At the present time, PyMOL is only useful for this when used in combination with external tools like GROMACS, MMTK, and Szybki. 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:wa...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Heinz-Uwe Hobohm > Sent: Monday, May 09, 2005 7:48 AM > To: Scott Classen; PyMOLBB > Subject: Re: [PyMOL] Homologous modelling > > Thanks for the replies on my "How to spoil PyMol for > modelling" request. Despite Peitzsch's SwissModel (very > convenient) and Sali's Modeller (less convenient but perhaps > more precise ?) I would like to know, for educational > purposes, whether PyMol could do reasonably well also. > > To be more precise; assume you apply a script like > > cmd.edit("(1NOT`3)",pkresi=1) > wizard mutagenesis > refresh_wizard > cmd.get_wizard().set_mode("ALA") > cmd.get_wizard().apply() > cmd.set_wizard() > > residue by residue according to the alignment, which further > (scriptable !) refinement steps are available in PyMol ? > > |