[Molvis-list] FirstGlance in Jmol: New Version

Eric Martz emartz at microbio.umass.edu
Wed May 3 22:45:34 EDT 2006

An enhanced version of FirstGlance in Jmol (version 0.99) is now available 
(http://firstglance.jmol.org). FirstGlance is free and open-source, as is 
the Jmol java applet upon which it is based. Major new features are:

1. There is a new Snapshot Gallery, which in effect provides a quick tour 
of what FirstGlance can do. http://firstglance.jmol.org/snaps/index.htm

2. "Contacts.." enables you to select any chain(s), residue(s), or atom(s) 
by clicking on them. It then shows you the probable non-covalent bonds to 
the selected moieties. The non-covalent bonds are divided into hydrogen 
bonds with water, water bridges, non-water hydrogen bonds, hydrophobic van 
der Waals interactions, cation-pi interactions, salt bridges and 
interactions with metals. These subsets can be shown one at a time, or in 
any combination. Distances and angles can be measured easily. See the 
Snapshot Gallery (above).

2. "Find.." lets you enter a sequence number (or range), or an amino acid 
name (such as PRO, CYS), or an element name. Whatever you enter is 
highlighted with yellow halos, making it easy to locate in the 3D 
structure. Gaps in protein chains (due to crystallographic disorder) can be 
located via a link to Wang & Dunbrack's Sequence-to-Coordinates (S2C) utility.

3. There is a new "one click" option to show all protein salt bridges and 
all protein cation-pi orbital interactions throughout the model (look under 
"More Views.."). A link to Gallivan and Dougherty's CaPTURE server provides 
a definitive list of energetically significant cation-pi interactions.

Many other improvements were made (see list at 

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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

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