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Re: [PyMOL] rotation of protein
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From: Chad D. <cha...@gm...> - 2011-02-28 12:06:31
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I thought symexp() would accomplish this, no? From: http://pymol.sourceforge.net/newman/user/S0400xtal.html Something like: fetch 3hhz symexp mysymm, 3hhz, (3hhz), 2.75 (I came up with 2.75 by trail-and-error as 2.5 generates no symmetry mates and 3.0 generated too many) In the case of 3m2m, the header you pasted shows there are 12 potential biological assemblies, 1 through 8 are all monomeric, however. 9 through 12 are the dimeric assemblies. If you need a dimer, you need to download any one of 9 through 12, which are probably all equivalent to one another. Note that PISA seems to believe that this is a monomer. I would be sure that you have other evidence that this is a dimer, as there are other crystal contacts in the deposited 3m2m. These might also help http://www.pymolwiki.org/index.php/Symexp http://www.pymolwiki.org/index.php/BiologicalUnit -Chad On Mon, Feb 28, 2011 at 12:20, kanika sharma <ksh...@gm...> wrote: > I have a dimeric protein 3HHZ.....to generate the dimer foll transformations > have to be made....the problem is that this is an identity matrix,so will > not change anything...can anyone help with this?? > how can i get the asymmetric unit to generate dimer?? > > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B > > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu > <hon...@bi...> wrote: >> >> Hi, Kanika, >> >> are you looking for biological units of proteins when you say stable >> dimer? If this is the case, I recommend the page: >> >> http://pdbwiki.org/index.php/Biological_unit >> at the bottom of the page you can find four very useful servers for the >> determination of biological units of proteins (PQS is not updated anymore): >> The Protein Quaternary Structure Server (PQS) [2] or [3] >> The Macro-Molecular Structure Database (MSD) [4] or [5] >> The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6] >> Protein quaternary structure investigation (PiQSi) [7] >> >> As a matter of fact, the PDB also provides the biological assembly of each >> PDB entry for download. More information can be found at: >> >> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html >> >> If your protein is not from the PDB, you can still try pisa ( >> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein >> coordinate files uploaded by the users and determines the "stable dimer" or >> else-mer of your protein. >> >> hope these help! >> hongbo >> >> On 02/25/2011 01:46 PM, kanika sharma wrote: >>> >>> Hi, >>> i am working to generate a dimer of my protein..I have made a duplicate >>> of my protein....Can any one tell me how to rotate my molecule to get >>> maximum stability..??? >>> >>> >>> Regards.. >>> Kanika >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>> data >>> generated by your applications, servers and devices whether physical, >>> virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> >>> >>> >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> -- >> Hongbo ZHU >> Postdoctoral Researcher >> Structural Bioinformatics >> >> Technische Universität Dresden >> Biotechnology Center >> Tatzberg 47/49 >> 01307 Dresden, Germany >> >> Tel.: +49 (0) 351 463-40083 >> Fax: +49 (0) 351 463-40087 >> E-Mail: hongbo.zhu@biotec.tu-dresden >> Webpage: www.biotec.tu-dresden.de > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |