Hi Kanika, In 3HHZ.pdb, I find:
REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 22-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, K, L, M, N, REMARK 350 AND CHAINS: O, R 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 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 So there are two BIOMT records. One identity, indicating that the coordinates as the are are also part of the biological assembly, and one giving the transformation to be applied to a copy. From the previous posts, you should already know how to do that... Cheers, Tsjerk On Mon, Feb 28, 2011 at 12:20 PM, kanika sharma <ksharma...@gmail.com> 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 > <hongbo....@biotec.tu-dresden.de> 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 (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> -- >> 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....@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 (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. 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