OK! Thank you, Eric! Right, and we can do all sorts of interesting things --
measure area, measure volume, pick out and visualize whatever ones we want,
adjust the VDW radii to suit (for example, to emphasize specific groups).
Most importantly, we can do just exactly what you describe -- show the
interaction in this interesting way. I happen to think the CONNECT option is
sort of interesting, but I don't know if that will catch on. Primarily what
is cool, in my mind, is how accessible this is. You can even use it right
now at the Protein Data Bank. All you do is open up a Jmol structure viewing
page there and then add this to your URL:
&JMOLJAR=
http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar
For example:
http://www.rcsb.org/pdb/explore/jmol.do?structureId=3HZ3&bionumber=1&JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar
Now, open a console and type something such as this into it:**
select not ligand
wireframe -0.1
color cpk
display within(group, within(5,ligand))
zoomto {ligand} 0
contact hbond {ligand}
or
contact hydrophobic {ligand}
or maybe
contact {ligand} parameters [0.5] NCI intermolecular
(We're still fine tuning those NCI parameters. Perhaps Julia can suggest
some adjustments there. I can see already that we need a MINSET parameter
there, and I see I should adjust the "hydrophobic" because I see it is
picking up the ionic interactions as well.)
Most importantly, this is all SO accessible. There is absolutely no reason
NOT to check it out, and we think it produces very nice definitely
publication-quality graphics in a matter of minutes.
By the way, I'm still working on a good way to fine-tune the graphics. I'm
thinking that a mode that allows rapid setting and moving of labels (set
picking LABEL, followed by clicking for a label and SHIFT for moving them)
plus maybe a double-click? to undisplay a group --
display displayed and not within(group, atomindex=_atomPicked)
We should think about what sets of commands would take care of this and get
them into the menu, maybe under "publication..."
Bob
On Wed, Jun 22, 2011 at 12:52 PM, Eric Martz <[email protected]>wrote:
> 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
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
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
