Technical Gallery
for FirstGlance in Jmol
Most users of FirstGlance in Jmol can skip this Gallery, which is provided to illustrate some technical aspects of FirstGlance in Jmol.

The PDB files below, with names ending .pdb, are bundled with FirstGlance in Jmol. The presence of .pdb in the filenames specified in the hyperlink query parameter "mol=" (see links), together with the absence of a filepath or http:// address, instructs FirstGlance to expect them in a subdirectory localPDBFiles of the directory that contains FirstGlance, on same server as FirstGlance. PDB codes specified without .pdb will be obtained from the Protein Data Bank.

In September, 2005, there were 955 published PDB entries containing protein but lacking HELIX, SHEET and TURN records (Jaime Prilusky, personal communication). That is about 3%.

ConSurf Examples:
PDB files modified by the ConSurf Server contain javascript and command scripts for Chime or Jmol in their headers. Examples in the FirstGlance Gallery illustrate the format, which is fully documented within Protein Explorer, under Presentations in Protein Explorer (PiPEs).
These files work in either Protein Explorer or in FirstGlance in Jmol. The filenames should contain "consurf". (The "_pipe" component of their filenames is required by Protein Explorer but is ignored by FirstGlance in Jmol.)

Tests for high numbers of sequence-identical chains:

Demonstrations of graceful handling of misformatted PDB files:

The links below test PDB file access methods, and demonstrate error handling.

Additional technical information will be found at the bottom of the page All About FirstGlance in Jmol.

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