[Molvis-list] FirstGlance in Jmol: Enhanced

Eric Martz emartz at microbio.umass.edu
Tue Apr 23 21:12:25 EDT 2013

I have today released a new version of FirstGlance in Jmol with many 
http://firstglance.jmol.org as always.

Formerly there was a single upper left control panel. Now there are 4 
tabs in the control panel: Molecule (labeled with the PDB code), 
Views, Tools, and Resources.

The Molecule tab is entirely new. It digests and summarizes a lot of 
information from the PDB file. Resolution and Free R are "graded" to 
assist those who are not structural biologists in interpreting them. 
Missing residues are reported chain by chain, including counts of 
charged residues that are missing.

The initial view has been modified to include "empty baskets" in the 
regions where residues present in the crystal are missing in the 
model due to disorder. Thus you can no longer be unaware when there 
are missing residues.

There is a clickable list of ligands and non-standard residues with 
their full names.

The "Find" tool now supports finding sequences, e.g. sequence=rgd 
will highlight (and count) all Arg Gly Asp sequences present in all 
chains. Ditto for nucleotide sequences.

The biological unit (quaternary structure) is more readily available 
and more help is provided.

Former versions of FirstGlance reported no counts. This version 
reports counts of many things, including chains, amino acids, 
nucleotides (total and per chain), lengths of chains, missing 
residues, missing charged residues, numbers of each 
ligand/non-standard residue, disulfide bonds, and anything found with 
the "Find" tool.

There are many new convenience features.

A more complete list of enhancements is here:

If you have suggestions for improvements, please do let me know!

There are undoubtedly bugs. Please report anything that looks 
dubious, being sure to include the PDB code you were using.


P.S. I have not undertaken a JSmol version yet.

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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://Martz.MolviZ.Org

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