Dear Bob, This is indeed very exciting! Kinemages and KiNG (by David and Jane Richardson) http://kinemage.biochem.duke.edu/
use a similar display to show "bumps" or "clashes", namely volumes where the van der Waals radii of atoms overlap (and hence the atoms are impossibly close). This is one of the most powerful features of KiNG. The display is similar to your example "contact DENSITY 0.2 HBOND". The Richardson's MolProbity server is one of the most powerful (and unique) protein model quality assessment tools. http://molprobity.biochem.duke.edu/ Among many other things, MolProbity first adds hydrogen atoms (enabling "all-atom contact analysis"), and then finds all clashes in a macromolecular model and constructs a kinemage (viewable in the java applet KiNG) to show them. It then calculates an overall clashscore, and compares this to the clashscores of other entries in the PDB with similar resolution. A bad clashscore means the model is iffy. It seems that Jmol is now close to doing a similar display. This would be fantastic! You can see a snapshot of their graphics for an hbond (green) and a bad clash (red) here: http://www.umass.edu/molvis/tmp/king-snaps/hbond-clash.png The hbond is between a hydrogen and a main-chain oxygen. The clash is between two hydrogens. They color "bad overlaps" red. They also show small overlaps as yellow and orange: http://www.umass.edu/molvis/tmp/king-snaps/small-overlaps.png And vdW contacts as green/blue: http://www.umass.edu/molvis/tmp/king-snaps/vdw.png The rotatable KiNG with checkboxes for 1d66, from which the above snapshots were taken, is here (server is slow today, be patient) http://molprobity.biochem.duke.edu/viewking.php?MolProbSID=344oifg8bqtuhlpommroicf6e6i4mvtg&url=data/344oifg8bqtuhlpommroicf6e6i4mvtg/kinemages/1d66FH-multi.kin.gz or try this http://tinyurl.com/43bfzth Here is the clashscore page: http://molprobity.biochem.duke.edu/index.php?MolProbSID=344oifg8bqtuhlpommroicf6e6i4mvtg&eventID=87 or http://tinyurl.com/3wm7hxg -Eric At 6/22/11, Robert Hanson wrote: >Jmol users -- > >Not "big" as in lots of bytes, but BIG in terms of impact. I believe >Erik Wyatt (undergraduate at St. Olaf) and I have cracked the >nonbonding interations nut. With this announcement we hereby >introduce what I just checked in as Jmol 12.1.51_dev: the CONTACT >command. This new command displays objects that float in space >between two interacting atoms. These could be hydrophobic >interactions or hydrogen bonds or in principle any other >interactions. A set of "teasers" can be found at ><http://stolaf.edu/people/hansonr/jmol/contact/2bxa.htm>http://stolaf.edu/people/hansonr/jmol/contact/2bxa.htm > > [snip] ------------------------------------------------------------------------------ Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Data protection magic? Nope - It's vRanger. Get your free trial download today. http://p.sf.net/sfu/quest-sfdev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
