[Molvis-list] PE highlights substructures noted in the PDB file header

[Eric Martz]

Dear Inbal,

I wanted to add another thought, which may interest others as well.

If I understand, your server will generate custom PDB files and display 
them in Chime. You could also offer a link to display them in Protein 
Explorer (PE) with a possible advantage explained below.

PE now has a control panel named "Features of the Molecule". It has buttons 
that highlight substructures designated in the header of the PDB file, e.g. 
specific residues comprising an active site or atoms comprising a ligand.

Thus, if you customize the header of a PDB file by adding SITE, REMARK 800 
(SITE_IDENTIFIER, SITE_DESCRIPTION) or HET, HETNAM, HETSYN, FORMUL records, 
buttons describing and showing the designated substructures will appear 
automatically in PE.

When such a customized-header PDB file is saved from Chime, the customized 
header is saved with it. When later displayed in PE, the buttons to 
highlight specified substructures are automatically generated in PE's 
Features of the Molecule control panel. The only customized file that needs 
to be downloaded is the PDB file. (If PE is also downloaded, the custom 
substructures will be described and highlighted entirely off-line.)

EXAMPLES are in the BioMolecular Explorer 3D that Frieda Reichsman and I 
recently announced here. We customized the headers of PDB files for 
hemoglobin and lactase. The links to display these molecules in PE will 
automatically offer descriptions and buttons to highlight functionally 
important substructures when you get to Features of the Molecule in PE.

http://www.umass.edu/molvis/freichsman/bme3d/Explorer3D_materials/explore.html#Hemoglobin

http://www.umass.edu/molvis/freichsman/bme3d/Explorer3D_materials/explore.html#Lactase

Technically, the way this works is that PE sends a "show pdbheader" command 
to Chime, which replies with the entire PDB file header via 
messageCallback(), which is captured as a javascript string. The header is 
parsed and buttons and labels generated accordingly.

Although PE will not be ported to Jmol for some while, Jmol already has the 
"show pdbheader" command and so a similar scheme could already be 
implemented using Jmol.

In future releases of PE, I plan to extend this scheme to presentations. 
The entire content of a presentation will be specified in the header(s) to 
the PDB file(s). Saving the PDB file(s) and playing it back in PE will 
display the authored presentation (as a fully customizable control panel 
within PE), as well as access to generic PE control panels. This is 
demonstrated at 
http://www.umass.edu/microbio/chime/beta/pipes/pe_pre2.15/pipes/2g12/index.htm 
but PE with this capability is not yet fully implemented or documented, so 
not yet publically released.

-Eric

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Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz