[Molvis-list] pdb-l: [Jmol-users] FirstGlance version 0.98 released

Eric Martz emartz at microbio.umass.edu
Sat Mar 11 22:53:10 EST 2006

I have updated FirstGlance in Jmol to version 0.98 
(http://firstglance.jmol.org). All previous URL's and links will 
automatically utilize the new version, although clearing the cache of your 
browser is recommended.

This new version enables you to hide portions of the structure easily. For 
example, an advance online publication in Nature Struct. Mol. Biol. (NSMB, 
http://www.nature.com/nsmb) reports 2ES4. Here, hiding all protein makes it 
easy to see the considerable range of ligands present. But you can also 
hide arbitrary subsets of chains, residues, or even atoms by clicking on 
them. Moieties so-hidden remain hidden in all views, until explicitly 

Thanks to Jaime Prilusky, you can now upload PDB files from your computer.

The importance of looking for specific oligomers has been emphasized by 
adding a prominent PQS button (Probable Quaternary Structure server at EBI, 
provided by Kim Henrick and Janet Thornton). PQS also gives you a single 
copy when the asymmetric unit (published PDB file) contains more than one 
copy of the molecule via crystal contacts. This is the case for the 
above-mentioned 2ES4, as well as 2B2A, 2FIF, 2D3G, and 2F8O in the March 
issue of NSMB. 1R0D in the February issue is noteworthy for having eight 
copies. A dramatic example of a specific oligomer (from the FirstGlance 
Gallery) is 1K28. PQS conveniently provides links to FirstGlance for 
displaying the single copy or oligomer it constructs.

"More Views.." now has help for evaluating model quality, and can also 
display the crystal unit cell, the bound box, or the coordinate axes. It 
also has a new link to a server that displays protein dipole moments in 
Jmol (provided by Clifford Felder, Joel Sussman, and Jaime Prilusky).

Planned for future version 0.99 are an automated view of contacts to any 
designated moieties, and location of residues specified by sequence number. 
Planned for future version 1.00 is support for translations to Spanish and 
other languages. Release dates for these versions are uncertain.

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

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