They won't work if your data does not have occupancy information. Please
check the latest version, and/or send me the offending file so I can check
it out.
On Mon, Jun 20, 2011 at 5:53 PM, Michael Evans evan...@illinois.edu wrote:
Lords lasses of Jmol—in several versions of Jmol 12.0 (at least
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
ps -- references at that bottom are to an alternative method of
visualization: We have incorporated into Jmol the promolecular NCI --
Noncovalent interactions -- calculation published recently in JACS[1] and
JCTC[2] by the Yang group at Duke. (The results of SCF NCIPLOT output are
also
I just refreshed my Jmol version, to no avail. See attached for one example
of a file that doesn't work (although none work for me right now; at least
none that I've created with WebMO http://www.webmo.net/).
Cheers, Mike
On Wed, Jun 22, 2011 at 1:37 AM, Robert Hanson hans...@stolaf.edu wrote:
OK, Mike. It was a simple bug fix. Jmol just wasn't processing the orbital
occupancy data correctly. See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip for the fix.
I've also fixed that in Jmol 12.0, but that release will be later this week
or next week, probably.
ps: WebMO uses
Thanks, Bob. Can't fault WebMO for using the best 3D visualization software
on the web!
Cheers, Mike
On Wed, Jun 22, 2011 at 9:49 AM, Robert Hanson hans...@stolaf.edu wrote:
OK, Mike. It was a simple bug fix. Jmol just wasn't processing the orbital
occupancy data correctly. See
Dear Jmol users,
Is there a way to link a jmolCheckbox to a non-Jmol checkbox? Just like what
jmolSetCheckboxGroup can do to several jmolCheckboxes.
Thank you.
Yingjie Lin
Mount Sinai School of Medicine
--
Simplify
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
I use Jmol to display atomic and molecular orbitals and it works well. I would
like to be able to render simple atomic orbitals 1s, 2s, 2p as electron density
maps made up of dots.
Is this currently possible and if so what sort of input file would work best?
Something like this
On 6/22/2011 2:23 PM, Greeves, Nick wrote:
I use Jmol to display atomic and molecular orbitals and it works well.
I would like to be able to render simple atomic orbitals 1s, 2s, 2p as
electron density maps made up of dots.
Is this currently possible and if so what sort of input file would
Hell Martin
Easy! The 2nd parameter in jmolApplet can take any commands, not just load.
So,
jmolApplet(400, load 1PDB.pdb; axes on; boundbox on;);
--
Simplify data backup and recovery for your virtual
Hello Yingjie
Not sure what you mean exactly, but...
jmolCheckbox() inserts a checkbox. You can include javascript commands as part
of the JmolScript there, if you wish.
Alteratively, you write the source code for a checkbox and include a
jmolScript(etc.) call in the
onClick() or
Many thanks. I couldn't get the precise syntax you suggest to work but from
Bob's examples (which I must have been subliminally aware of) but
zap;isosurface phase scale 0.5 atomicOrbital 2 1 0 POINTS 10
worked fine.
Maybe it was the Zeff value that disagreed with my file which is the hydride
Wonderful, do you mind pointing me to where I can read about this?
So instead of writing commands explicitly into the jmolApplet
constructor call, I can write the path to a Jmol script?
Eg.
jmolApplet(400, ../jmolScripts/jmolScriptToDisplayBox.js);
?
Am 22.06.11 20:50, schrieb Angel
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
wow. that's a HECK of a lot of dots. That actually works?
On Wed, Jun 22, 2011 at 2:05 PM, Greeves, Nick ngree...@liverpool.ac.ukwrote:
Many thanks. I couldn't get the precise syntax you suggest to work but from
Bob's examples (which I must have been subliminally aware of) but
zap;isosurface
On 22 Jun 2011 at 22:11, Martin Hediger wrote:
Wonderful, do you mind pointing me to where I can read about this?
http://jmol.sourceforge.net/jslibrary/#jmolApplet
So instead of writing commands explicitly into the jmolApplet
constructor call, I can write the path to a Jmol script?
Eg.
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