I have today released a new version of FirstGlance in Jmol with many enhancements. http://firstglance.jmol.org as always.
Formerly there was a single upper left control panel. Now there are 4 tabs in the control panel: Molecule (labeled with the PDB code), Views, Tools, and Resources. The Molecule tab is entirely new. It digests and summarizes a lot of information from the PDB file. Resolution and Free R are "graded" to assist those who are not structural biologists in interpreting them. Missing residues are reported chain by chain, including counts of charged residues that are missing. The initial view has been modified to include "empty baskets" in the regions where residues present in the crystal are missing in the model due to disorder. Thus you can no longer be unaware when there are missing residues. There is a clickable list of ligands and non-standard residues with their full names. The "Find" tool now supports finding sequences, e.g. sequence=rgd will highlight (and count) all Arg Gly Asp sequences present in all chains. Ditto for nucleotide sequences. The biological unit (quaternary structure) is more readily available and more help is provided. Former versions of FirstGlance reported no counts. This version reports counts of many things, including chains, amino acids, nucleotides (total and per chain), lengths of chains, missing residues, missing charged residues, numbers of each ligand/non-standard residue, disulfide bonds, and anything found with the "Find" tool. There are many new convenience features. A more complete list of enhancements is here: http://firstglance.jmol.org/versions.htm If you have suggestions for improvements, please do let me know! There are undoubtedly bugs. Please report anything that looks dubious, being sure to include the PDB code you were using. Eric P.S. I have not undertaken a JSmol version yet. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org FirstGlance, used by Nature - http://firstglance.jmol.org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Interactive Molecules in Public Spaces http://MolecularPlayground.Org Workshops: http://workshops.molviz.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
