Re: [Jmol-users] Applying symmetry operations with Jmol?

[Bob H. <ha...@st...>]

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 <em...@mi...> 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.
>
>
>
>  
>
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>>    
>>
>
>
>  
>


-- 
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