Eric and Dan, This what you're looking for?
http://www.stolaf.edu/people/hansonr/temp/1sva.jpg load 1sva.pdb filter "*.CA;BIOMOLECULE 1;APPLY SYMMETRY" color chain select * 123420 atoms selected rotation and zooming and rendering is very fast; commands are slow, I think because it is automatically saving the state, and I need to figure out how to turn that off. not cloninng bonds, yet. version=11.5.32 # new feature: load [file info] FILTER "[filter string]" # new feature: load [file info] FILTER "BIOMOLECULE n" # new feature: load [file info] FILTER "BIOMOLECULE n;APPLY SYMMETRY" # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n" # # The first format loads only those atoms matching a specific filter or set of # filter terms -- only a crude filter here, only for PDB and CIF files: # # *.XX an atom name, such as .CA # *:X a chain ID # *^X an insertion code # *%X an alternative location code # # multiple matches are allowed -- implied AND: # # load "1sva.pdb" FILTER "*.CA;*:1;*:2" ## # also, for PDB files, "BIOMOLECULE 1" automatically selects for the chains listed for biomolecule 1 # in REMARK 350, and APPLY SYMMETRY applies the symmetry as described in those REMARKS # Bob Dan Bolser wrote: >On 26/04/2008, Eric Martz <[EMAIL PROTECTED]> wrote: > > >> Thank you, Rolf, for explaining biological units. It will be tremendously >>useful if Jmol can generate them, when asked via script commands, from the >>symmetry operations in the PDB (REMARK 350) or mmCIF file header. >> >> I just wanted to add a few points. >> >> 1. VERY LARGE BIOLOGICAL UNITS. In some cases, notably virus capsid >>proteins, the biological unit is very large (e.g. an entire virus capsid). >>As an all-non-hydrogen atom PDB file, these can easily exceed 100 megabytes. >>An example would be 1sva, a capsid protein from Simian Virus 40. >> >> Thus, if Jmol is enabled to use REMARK 350 (or the equivalent in mmCIF), >>there will need to be some mechanism to handle cases where the result would >>exceed the capacity of java memory. Hopefully this can be done gracefully, >>rather than just staying blank forever or freezing/crashing. >> >> In my tests long ago with Jmol applet 10.00.46 ( >>http://molvis.sdsc.edu/fgij/bigpdb.htm ), Jmol applet >>failed to display PDB files containing about 200,000 atoms (3ezb with 40 NMR >>models, a 17 megabyte PDB file uncompressed), but displayed 1jj2, which >>contains 98,000 atoms (an 8 megabyte PDB file uncompressed). I attributed >>this cutoff to a java memory issue. >> >> >> 2. BIOLOGICAL UNITS SMALLER THAN THE ASYMMETRIC UNIT. Sometimes the >>asymmetric unit (what is published in the PDB file) contains more than one >>biological unit. It would be ideal if Jmol could handle these as well. It >>could either show only the first biological unit, or possibly could set them >>up in its memory as separate models or frames. An example is 1b6b, which >>contains a homodimer. The dimerization is believed to be a artifact of >>crystallization. Thus, there are two biological units in the asymmetric unit >>(PDB file). At >>http://www.pdb.org/pdb/explore/explore.do?structureId=1B6B >>you will be shown static snapshots of the asymmetric unit, and each monomer. >> >> The requirement to separate the chains is indicated thus in the PDB format: >> >> >> REMARK 350 GENERATING THE >>BIOMOLECULE >>REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE >>KNOWN >>REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF >>THE >>REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT >>TRANSFORMATIONS >>REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC >>AND >>REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE >>GIVEN. >>REMARK >>350 >> >>REMARK 350 BIOMOLECULE: >>1 >>REMARK 350 APPLY THE FOLLOWING TO CHAINS: >>A >>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 BIOMOLECULE: >>2 >>REMARK 350 APPLY THE FOLLOWING TO CHAINS: >>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 >> >> >>Incidentally, even when you are viewing the snapshot of the biological unit >>at RCSB, clicking on the visualizers (e.g. KiNG, Jmol, etc.) does NOT show >>you the biological unit. To get it, you must use the Structure tab (upper >>left), then open Download Files, and the last item(s) will be the biological >>unit(s), gzipped. >> >> A series of examples of different outcomes of biological units is given at >>http://proteinexplorer.org/pqs.htm >> This document first explains the operation of the Probable Quaternary >>Structure (PQS) Server at the European Bioinformatics Institute, and then >>gives the examples. >> >> PQS examines the contacts within the crystal, and makes an automated >>judgement as to whether each contact is the result of a co-evolved specific >>oligomeric interaction (large area, often hydrophobic core and/or salt >>bridges), or alternatively is an artifactual "crystal contact" (small area >>between hydrophilic surfaces). It is usually correct, but sometimes wrong. >>It works only when the biological unit forms in the crystal (the usual case, >>but not always). >> >> PQS is in the process of being superceded by a new algorithm implemented as >>a server named PISA. >> >> -Eric >> >> > >Hi all, > >Looks like a very useful thread! Below are a few comments. > >Eric: I was thinking *exactly* the same thing! ;-) > >Bob: Some friends and I tried to answer that question (what is a >BioUnit?) as part of a 'PDB FAQ' that we have been working on. We >thought that this question was important and complex enough to get a >page all to itself. You can see what we currently have here: > >http://pdbwiki.org/index.php/Biological_unit > > >The PDB FAQ may be of general interest to this list. It can be found here: > >http://pdbwiki.org/index.php/PDB_FAQ > > >The FAQ is part of a PDB-Wiki project that we announced on PDB-L: > >https://lists.sdsc.edu/pipermail/pdb-l/2008-April/004321.html > > >Rolf / Eric: Thanks for the information about BioUnits. If it is OK >with you I will try to incorporate your comments into the above FAQ >article? Or if you are really keen, you are free to edit the article >yourself! > >Eric: I just realized, probably the easiest way to get the BioUnit >data is to use the biounit division of the PDB FTP site: > >ftp://ftp.wwpdb.org/pub/pdb/data > > >Under this branch you can find exactly the data that you want. Namely, >the results of applying the symmetry operations in remark 350 to the >ASU. > > >Note that there are many errors in the biounit division of the PDB. >Trivially these include things like dimers that are *not* dimers under >physiological conditions, monomers that *are* dimers under >physiological conditions etc., etc. This is why the 'databases of >predicted protein quaternary structures' are so important. My favorite >is PiQSi: > >http://www.supfam.org/elevy/piqsi/piqsi_home.cgi > > >I hope the above helps. Thanks all for the replies, > >Dan. > > > > > >>------------------------------------------------------------------------- >> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >> Don't miss this year's exciting event. There's still time to save $100. >> Use priority code J8TL2D2. >>http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >>_______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> > > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. 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