As announced yesterday, FirstGlance 0.99 is, at last, completed (he says
confidently, and surely hopes) and released (http://firstglance.jmol.org).
It uses Jmol 10.2.0. I have tested it in Windows MSIE & Firefox, and Mac
OSX 10.3.9 Safari and Firefox. It is downloadable
(http://bioinformatics.org/firstglance)
I spent several more weeks working on this version since I made a preview
of version 0.99 available on April 13. The following have been added since
then:
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
Regarding the next two items, I wanted to avoid having any important part
of the model be invisible.
2. Isolated standard residues (such as a single amino acid, or a single
nucleotide) were invisible. These are often given a "chain" name (although
there is only residue in the "chain") but are invisible in backbone
displays (Cartoon, Secondary Structure, N->C Rainbow). These are typically
important ligands, but because they are standard residues, are not
automatically deemed "ligand". Using the new Jmol command "connected" in
Jmol 10.2.0 (THANKS to the Jmol team!), I was able to select such isolated
residues and include them in "Ligands+", thereby spacefilling them in the
initial view. Examples are GLY1 in "chain" G in 4CPA, and Adenosine 351 in
"chain" B in 1BKX. A full explanation, and a synthetic PDB file
demonstrating all handled cases, is at
http://firstglance.jmol.org/bbinvis.htm
3. Another category of "invisible" or improperly rendered atoms are those
that Jmol does not recognize either as (protein or nucleic acid) nor as
"hetero". These can be selected with the command "select not
(protein,nucleic,hetero)". Although rare, they should not be invisible. In
FirstGlance, I have termed these "anomalous atoms" and they are now shown
in the initial view as dot surfaces. New rendering options for anomalous
atoms are now under "More Views..". An example is 1AL4 (newly included in
the Technical Gallery). A complete explanation is at
http://firstglance.jmol.org/notes.htm#anomalous
4. I added "water bridges" as a seventh category of non-covalent bonds to
the Contacts.. display. Very cool!
5. The list of probable bugs in Jmol that affect FirstGlance is now
completed, to the best of my knowledge:
http://firstglance.jmol.org/bugsjmol.htm
I have implemented workaround code in FirstGlance that produces
satisfactory results in most cases. (Well, there may be one more subtle
bug Frieda and I are working to define -- new in 10.2.)
6. The complete list of changes between FirstGlance 0.98 and 0.99 is here:
http://firstglance.jmol.org/versions.htm
Many smaller improvements were made that are not listed there.
Let me know if anything seems amiss!
-Eric
----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz
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