Technical Gallery for FirstGlance

Technical Gallery
for FirstGlance in Jmol
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Caution This document has not been updated since version 1.0 of FirstGlance in Jmol (December, 2006). It is awaiting updating for the current version 4.1 (September 18, 2022) and a much improved 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.

incsides.pdb: Incomplete sidechains for all 20 amino acids. Synthetic test file derived from 4MDH. Many are spacefilled in the initial view because they are isolated residues, unconnected to others via peptide bonds. More..
1AL4: Gramicidin, a small molecule example with alternate locations for some residues (not yet well handled by FirstGlance). The alternate locations are most easily seen in the Vines view, checking More Detail and also checking hide hydrogen atoms. Then hide Ligands+ with the toggle button,
1VCX: Rubredoxin by neutron diffraction. Partially deuterated. Most of the water is DOD. There is also D on protein, but "select deuterium" does not work. "select hydrogen" works. See Bugs.
bb-invis.pdb: Tests display of standard residues invisible in backbone displays. Includes single residue "chains". More..
1pgb-ss.pdb: 1PGB with HELIX, SHEET, TURN records deleted. Jmol determines secondary structure. Compare with 1PGB in the main Gallery where the authors have specified the secondary structure.
1sva-cao.pdb: SV40 virus capsid (alpha carbon atoms only, 123,000 atoms, 9 megabytes).
Caution, this file may be too large for the available java memory on some computers. See also Files Too Big for Jmol. Some FirstGlance view links fail intermittantly, apparently due to the size of this data file.

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:

1flo_consurf_6chains.pdb.gz: Copy pretending 6 identical chains.
1flo_consurf_7chains.pdb: Copy pretending 7 identical chains.

Demonstrations of graceful handling of misformatted PDB files:

2vaa_con_surf.pdb: Lacks "consurf" in PDB filename. Default FirstGlance molecular view will display, followed by the ConSurf view. (See comments at top of msgcall.js for explanation.)
1d66_consurf.pdb: PDB file with "consurf" inappropriately in filename. No PiPE block in header. After a brief delay, the default FirstGlance molecular view will be shown.
2hu4_consurf1162594776_pipe.pdb: TEMPORARY TEST consurf oct 06

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

http://molvis.sdsc.edu/pdb/bilagram.pdb: Theoretical model of lipid bilayer with gramicidin channel.
Not available from the Protein Data Bank. Demonstrates handling of an absolute URL in contrast to a PDB Id code.
ftp://www.bio.umass.edu/pub/shareware/rasmol/fourmols/bilagram.pdb: Theoretical model of lipid bilayer with gramicidin channel.
Not available from the Protein Data Bank. This URL uses an FTP (rather than HTTP) protocol. Unsigned Jmol cannot process FTP requests, so this URL demonstrates how FirstGlance attempts to handle such a URL gracefully.
../pdb/dna_b_form.pdb: B Form DNA.
Demonstrates handling of a relative URL in contrast to a PDB Id code. (Fails ungracefully if the PDB code does not exist in the specified directory, or if the unsigned applet is in use, and the file is inaccessible to it.)
4phv.pdb: HIV protease complexed with inhibitor.
When a filename ends in .pdb, but lacks a path, it is assumed to be in the directory localPDBFiles bundled with FirstGlance. Unlike 1pgb-ss.pdb (see link above), 4phv.pdb does not exist in this directory, so this test link is intended to fail to load the molecule. FirstGlance cannot anticipate or detect the absence of this file, hence the failure will be ungraceful.

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

Feedback to the FirstGlance Development Team.