[Jmol-users] BIG addition to Jmol -- CONTACT command

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

Re: [Jmol-users] BIG addition to Jmol -- CONTACT 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 visualizab

Re: [Jmol-users] MO HOMO/LUMO?

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 ). Cheers, Mike On Wed, Jun 22, 2011 at 1:37 AM, Robert Hanson wrote: > They won't work

Re: [Jmol-users] MO HOMO/LUMO?

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 J

Re: [Jmol-users] MO HOMO/LUMO?

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 wrote: > OK, Mike. It was a simple bug fix. Jmol just wasn't processing the orbital > occupancy data correctly. See > http://chemapps.stolaf.edu/j

[Jmol-users] linking a jmolCheckbox to a non-Jmol checkbox

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 dat

Re: [Jmol-users] BIG addition to Jmol -- CONTACT command

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 o

[Jmol-users] Electron density maps - dots

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 http://ursula.ch

Re: [Jmol-users] Electron density maps - dots

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 wor

Re: [Jmol-users] How to introduce coordinate system

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 environm

Re: [Jmol-users] linking a jmolCheckbox to a non-Jmol checkbox

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 onChange()

[Jmol-users] Electron density maps - dots

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

Re: [Jmol-users] How to introduce coordinate system

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 Herráe

Re: [Jmol-users] BIG addition to Jmol -- CONTACT command

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 i

Re: [Jmol-users] Electron density maps - dots

wow. that's a HECK of a lot of dots. That actually works? On Wed, Jun 22, 2011 at 2:05 PM, Greeves, Nick wrote: > 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 atomic

Re: [Jmol-users] How to introduce coordinate system

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.