The JenaLib offers a new
QuickSearch Option
for PDB, NDB, UniProt and PROSITE codes as well as for other search strings.
Due to an automatic recognition mechanism only one input field is required.
On the atlas pages information on both asymmetric and biological units is now provided.
Also, in the JenaLib Jmol viewer asymmetric and biological units
can be visualized on an equal footing.
So, one can, for example, color complete biological units according to SCOP domains.
Thus far, information on biological units is exclusively taken from the PDB.
The atlas pages offer, however, a link to the
PQS Protein Structure Quaternary Server at the EBI.
New color schemes are now available for coloring according to asymmetric units and chains.
Coloring by Chain(Asym. Unit) assigns equal colors to symmetry-related
chains, whereas Chain(Biol. Unit) colors each chain with a different color. Coloring by Asymmetric Unit assigns
a specific color to each asymmetric unit that may consist of one or more chains.
Finally, mapping of PROSITE patterns and SNPs is now also available for
biological units.
The PDB offers for NMR structures both the original PDB file and a file with so-called 'biological unit coordinates'.
As compared to the original PDB file the latter file usually contains the very same structural data, but has a shortened header, occasionally renamed chain identifiers and possibly also corrections.
Information from both file types is available on the atlas pages and in the Jmol viewer.
Because we believe that the term 'biological unit' is misleading we have designated this second NMR structure file type by an asterisk.
The thumbnail images on the atlas pages show for proteins asymmetric units and for nucleic acid-containg structures biological units.
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Note:
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Biological unit files can be very large. To give a hint on the memory requirements for visualization with 'Jmol', the compressed size
of each PDB file is provided (example: Biological Unit 1 (400 KB) ). The file is transferred to 'Jmol'
in this compressed form.
The uncompressed size is about 10 times as high, about 4 Megabytes in the above example.
As a Java applet 'Jmol' shares the available memory with all other Java programs and applets.
By default this is often limited by the 'Java Virtual Machine' (JavaVM) to 96 Megabytes. This may cause problems for the Jmol Viewer in the case of very large structures.
One example is the structure of the Pariacoto Virus (PDB code :
1f8v).
The biological unit of the virus contains 60 copies of the asymmetric unit and the corresponding compressed filesize is 10.1 Megabytes.
One can change the memory siye in the advanced options of JavaVM
[Control Panel/Java/Java Control Panel/Java Applet Runtime Settings/Java Runtime Parameters]. '-Xmx256m' would, for example, set the maximum available memory to 256 Megabytes.
The maximum possible value value is only limited by the amount of physical and virtual memory available on a particular computer. More information on this can be obtained from the JavaVM manual. In any case it is a good idea to have only one Java application running.
By increasing the JavaVM memory size it was possible to visualize the above-mentioned
structure with Jmol on a notebook with a 1.6 GHz processor and 512 Megabytes RAM (needs patience, however).
The generation of atlas pages will take some time if extensive information from the data base is required. This refers in particular to entries for which a large number of related entries sharing the same UniProt ID is available (example: 5lyz) or if the the structure consists of a large number of chains, like for the ribosomes (example: 1ffk).
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New features 'Age Related' and 'OMIM' for customizing entry lists - December 13, 2006
New 'QuickSearch' option and 'Biological Unit' integration - April 27, 2006