[Molvis-list] FirstGlance in Jmol 2.3 released

Eric Martz emartz at microbio.umass.edu
Tue Jun 16 16:55:16 EDT 2015

FirstGlance in Jmol version 2.3 has been released today 
(FirstGlance.Jmol.Org <http://firstglance.jmol.org>). FirstGlance in 
Jmol is an easy-to-use yet powerful, free, open-source macromolecular 
visualization package. New structures published in /Nature/ (and several 
/Nature/ specialty journals) can be explored in FirstGlance by clicking 
the [3D] buttons in online articles. FirstGlance is offered by a number 
of value-added servers, including ConSurf <http://consurf.tau.ac.il>, 
ExPASy <http://www.expasy.org/cgi-bin/get-pdb.pl?3ckz>, Orientations of 
Proteins in Membranes <http://opm.phar.umich.edu/>, and Proteopedia.Org 

For example, 3v6t is a DNA-binding TAL (transcription activator-like) 
effector protein from phytopathogenic bacteria bound to DNA*. In 
addition to showing the main structural features, FirstGlance 
immediately alerts you to the 20 missing residues and 3 residues with 
incomplete sidechains, as well as rating its Rfree as "better than 
average at this resolution".

View 3v6t in FirstGlance in Jmol 

In its initial view, FirstGlance indicates missing residues and missing 
sidechains as well as giving each chain of the asymmetric unit a 
distinct color, and showing ligands with spacefilling atoms. It 
interprets Rfree using average and outlying values at the same 
resolution in the PDB. It lists ligand full names and counts and 
indicates their locations in one click. It offers biological unit 
quaternary structures through the MakeMultimer 
<http://watcut.uwaterloo.ca/tools/makemultimer/> server. Any moiety of 
interest can be isolated in a single click (hiding the remainder of the 
model). Disulfide bonds, salt bridges, and cation-pi interactions are 
shown with a few clicks. Sequence numbers or motifs are easily found. 
The asymmetric unit is decorated with all crystal contacts in a single 
click, and easily colored by B-factor/temperature. Non-covalent 
interactions to any moiety are easily visualized, and divided into seven 

FirstGlance in Jmol runs in all popular browsers in Windows, OS X and 
linux. It does not need Java, but will perform better with Java should 
you wish to install it.

New in version 2.3:
  - All residues can be labeled with their sequence numbers and residue 
  - A practical guide to homology modeling. Homology models can be 
uploaded to FirstGlance.
  - An index to help you find where a view or tool can be found, or how 
to see something of interest.

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

  * Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
  * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
  * Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
  * Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
  * Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
  * Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
  * Interactive Molecules in Architectural Spaces:
    MolecularPlayground.Org <http://molecularplayground.Org>
  * Workshops: Workshops.MolviZ.Org <http://workshops.MolviZ.Org>

*Thanks to David Goodsell's Molecule of the Month 

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