Hi Chad, Kanika, Symexp is for generating symmetry mates, not for (re)constructing biological assemblies.
If the BIOMT record gives an identity matrix, it means that there is no further information for building a biological unit. The biological unit is most likely contained in the PDB file. Note that it may be part of the structure in the PDB file, as those may contain an asymmetric crystallographic unit. Kanika, You come up with a different protein every time, which makes it a bit confusing for us, but probably also for yourself. Maybe it's good to first get to understand the basics, the file formats, biological units, pymol, etc. Otherwise, provide a more full account of what you're trying to do, what you've tried to do yourself getting there and where you got stuck. Cheers, Tsjerk On Mon, Feb 28, 2011 at 1:06 PM, Chad Davis <chad.a.da...@gmail.com> wrote: > 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 <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 >> > > ------------------------------------------------------------------------------ > 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. 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
