The JenaLib site has moved to it's separate domain jenalib.leibniz-fli.de; all requests to the JenaLib using "jenalib.leibniz-fli.de" or "www.leibniz-fli.de" should transparently get redirected to jenalib.leibniz-fli.de. Note that all JenaLib addresses and links on this page have been converted to the new site address.

An enhanced version of the JenaLib Jmol Viewer has been released as Jena3D.

Jena3D replaces the JenaLib Jmol Viewer within the JenaLib. Jena3D has its own homepage but is still closely linked to the JenaLib.

Jena3D also introduces a Sequence/Alignment viewer that is uncoupled from the JenaLib atlas pages.

Jena3D contains a mirror of the Jmol interactive scripting documentation.

Exon information from the ENSEMBL and UniProtKB databases is used to map exons onto PDB structures.

The JenaLib atlas pages now provide an exon mapping table with direct links to the corresponding ENSEMBL and UniProtKB pages.

The JenaLib Jmol Viewer now offers an exon standard view, highlighting exons and exon boundaries. These can also be adressed and highlighted individually by specific control elements.

See our review:

The JenaLib is now based on remediated PDB file data.

The PDB Remediation Project is a joint effort of the members of the wwPDB (RCSB PDB, MSD-EBI, PDBj, BMRB).
It aims to provide a uniform remediated structural dataset in all three file formats (PDB, mmCIF, PDBXML) that are used to distribute the Protein Data Bank (PDB).

An overview of the project and the resulting changes is provided in this PDF document.

The SCOP and CATH domain descriptions presented in the JenaLib were adapted to the remediated PDB data (e.g.: chain identifier " " changed to "A").

The JenaLib offers a new user-friendly SCOP and CATH structure classification Tree Browser.

It diplays either the SCOP or CATH classification hierarchy and provides control buttons to collapse/expand specific hierarchy levels at once. Each tree node can also be collapsed/expanded individually.

The atlas page of each PDB entry classified in SCOP/CATH contains the entry-specific part of the tree. By clicking on the name of any displayed hierarchy level (e.g.: GroES-like) the whole tree below this level can be explored with the Tree Browser.

At the top of the Tree Browser a SCOP or CATH search option is integrated.

Additionally the visualization of CATH domains was added to the Jenalib Jmol Viewer.

Information on the CancerSNPs reported in the article is integrated now into the JenaLib.

The 3508 CancerSNPs described by the authors were mapped onto PDB structures using information from the CCDS, ENSEMBL and
UniProtKB/Swiss-Prot databases.   (current mapping statistics)

The information of the GenAge database is integrated into the 'Customize Entry List' option of the JenaLib.

This allows to select PDB entry sets related to human ageing.

In addition, OMIM cross references from GenAge and UniProt are now included in the entry list customization scheme.

The JenaLib offers a new very versatile option for customizing entry lists.

Entry sets can be selected according to

• Database (PDB and/or NDB)
• Method (X-Ray/Neutron/Synchrotron, NMR, Electron, Other Experimental, Theoretical Model)
• Molecule type (Protein, DNA, etc.)
• Other structural features
  (ocurrence of modified residues, ligands/ions, single amino acid polymorphisms (SAPs), PROSITE motifs and SCOP domains)

The user can select the desired output columns (currently from a list of 26 columns) and it is also possible to sort the output according to information indicated in any of the columns.

The output format is either HTML or ASCII (tab-separated text).

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.

Note:

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).

The IMB Jena Image Library of Biological Macromolecules has served the scientific and educational communities for more than 10 years (since 1993).