[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
<http://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
<http://firstglance.jmol.org/fg.htm?mol=3v6t>.
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
categories.
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
names.
- 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
<http://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
<http://www.rcsb.org/pdb/101/motm.do?momID=180>!
More information about the Molvis-list
mailing list