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
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