From: Abhinav K. <abh...@sl...> - 2009-01-29 21:10:43
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Hi, Is there someway to select and show conserved residues when a bunch of superimposed structures are loaded into Pymol? And if so, can identical and similar residues be selected separately? -- Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 |
From: Robert C. <rob...@qu...> - 2009-01-29 22:47:54
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Hi Abhinav, On Thu, 29 Jan 2009 13:10:25 -0800, Abhinav Kumar <abh...@sl...> wrote: > Is there someway to select and show conserved residues when a bunch of > superimposed structures are loaded into Pymol? > And if so, can identical and similar residues be selected separately? I don't believe that there is a direct way to do it from the superimposition, but I commonly apply "external data" to the B-factor column of a PDB file for colouring purposes. For example, you could calculate the degree of sequence conservation at each residue and colour on that. I use the following scripts: http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/variability.py http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/seq_convert.py http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py See the pages: http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/ and http://pldserver1.biochem.queensu.ca/~rlc/work/pymol for more information. When you align the structures, if you use the "object=" keyword (or do it using the "align" menu) it will create an alignment object that you can save as a Clustal format file. This file can then be used to calculate the sequence variability. Cheers Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Donnie B. <dbe...@ge...> - 2009-01-30 03:42:58
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On 13:10 Thu 29 Jan , Abhinav Kumar wrote: > Is there someway to select and show conserved residues when a bunch of > superimposed structures are loaded into Pymol? > And if so, can identical and similar residues be selected separately? I often use ConSurf, which will give you a PDB with a conservation index in the B-factor field. You can then load that into PyMol and color by B as usual. Since it's unclear exactly what you intend to do with this, I can't tell you whether ConSurf makes sense for your use. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com |