Re: [Jmol-users] SMARTS question

Eric, I’ve not used SMARTS before, so I tried your commands below: > rings6 = {*}.find("SMARTS","c1c1", true) select rings6 and > ringsh = {*}.find("SMARTS","c1cncn1", true) select ringsh Running the Jmol application, v. 14.8.0, and loading tryptophan via “load $tryptophan”, your

Re: [Jmol-users] Followup to "Re: vibrate.htm for Gaussian output?"

Hi, Pascal, A revised version is here: http://faculty.fairfield.edu/mkubasik/GaussianReaders/GaussianOutput.2017.html As you know, the original distribution comes with “vibrate.html”. My page is based heavily on that one, shown here:

Re: [Jmol-users] use of select bonds

Angel, I am unfamiliar with the syntax you are using. However, placing the bonds into a variable has worked for me, as in: select {oxygen and connected(1) and connected(carbon)} or {carbon and (connected(oxygen))} x1={selected}.bonds select x1 bondorder 2 select none I use the above code to

Re: [Jmol-users] Running Jmol in Linux command line

Huan, You can add a line to your .profile or your .bashrc to recognize an alias to run Jmol. For example, on my mac, I have edited my .profile to include: alias jmol144="java -jar /Applications/jmol-14.4.0_2015.12.02/Jmol.jar” This line means that typing jmol144 opens Jmol. Note that if you

Re: [Jmol-users] Best way to access getproperty with JSmol

Bob, Thanks to you and the team, for your ongoing development of JSmol! I think Mark’s initial approach was consistent with an orientation in the bioinformatics world of “grab-everything-and-sort-later.” It makes sense to do that…sometimes! Best, Matt

Re: [Jmol-users] Best way to access getproperty with JSmol

Mark, One other thing. You wrote that "when you load the model it prints all the vibrational energies out”. But here’s the thing…I think that, technically, the “names” of the models containing vibrations are printed, i.e., what you would get from x = getproperty("modelinfo.models.name”)

Re: [Jmol-users] Best way to access getproperty with JSmol

Dear Mark and Bob, Perhaps getting a large quantity of “auxiliarydata” is slowing things down? Maybe, Mark, you could drill down a bit to get the specific auxiliary data that you want. So, for example, maybe instead of var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo"); You could

Re: [Jmol-users] Potential bug in reading xyz files

Peter, On my editor, your “broken” file has an additional text (the letter “a’) on the first line. Could that be the problem? Matt Kubasik On Sep 26, 2016, at 6:46 AM, Peter Brommer > wrote: Hi, This concerns Jmol Version:

Re: [Jmol-users] Use of variable in a call to getProperty

How about here? http://wiki.jmol.org/index.php/Scripting/GetProperty On Jul 8, 2016, at 11:46 AM, Angel Herráez > wrote: Sure! The question is... where to locate it? Goes to the to-do list. Suggestions or actual page edition are welcome

Re: [Jmol-users] Use of variable in a call to getProperty

Thanks, Angel. I'm never sure about these things. Sometimes in my scripts I get "TRUE" when I'm expecting a numerical result. This makes me think I'm mixing types. Maybe I'm just mis-using built in functions. But that's for another thread! From: Herráez

Re: [Jmol-users] Use of variable in a call to getProperty

. 16 17:04, Kubasik, Matthew A. wrote: > Max, > Hi Matt, Thanks for your suggestions. > Two suggestions. > > First, something like: > > freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue') > > will look for frequency values of all models and

Re: [Jmol-users] Use of variable in a call to getProperty

Max, Two suggestions. First, something like: freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue') will look for frequency values of all models and put them in the array "freqvalues". Unfortunately, this array will have empty entries for models lacking frequency values.

Re: [Jmol-users] Wildcard for atom properties

@lists.sourceforge.net Subject: Re: [Jmol-users] Wildcard for atom properties On 06/22/2016 09:02 PM, Kubasik, Matthew A. wrote: > Rolf, > > Sorry, I switched conventions, which is confusing everything. > > So, yes, "print {atomno=3}.a?" works to print atom propertie

Re: [Jmol-users] Wildcard for atom properties

ect: Re: [Jmol-users] Wildcard for atom properties On 06/22/2016 08:25 PM, Kubasik, Matthew A. wrote: > Bob and List, > > Using the stand alone app on a Mac (10.11.5), I cannot seem to get the > wildcard for atom properties to work as I would expect from > > http://chemapps

[Jmol-users] Wildcard for atom properties

Bob and List, Using the stand alone app on a Mac (10.11.5), I cannot seem to get the wildcard for atom properties to work as I would expect from http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=14.6.0_2016.06.14#atomproperties. The doc says print {atomno=3}.a? will give the atom properties

[Jmol-users] Energies of "color hbonds energy"?

Bob and list, Are the energies used to color the hydrogen bonds, using the command “color hbonds energy”, available, say, in an array? Are the hbonds themselves indexed or arrayed in some way? Are atom properties, e.g., atomno, of atoms identified as participating in h-bonding available as in

Re: [Jmol-users] Energies of "color hbonds energy"?

Already answered: http://ehc.ac/p/jmol/mailman/message/31977259/ Thanks, Bob! Apologies to the list, MK On Jan 23, 2016, at 11:53 AM, Kubasik, Matthew A. <mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>> wrote: Oops…sorry, I see this was asked and answered six year

Re: [Jmol-users] Energies of "color hbonds energy"?

9 4096 1.0 -1.358 hbond; 70 42 4096 1.0 -1.674 hbond; 83 55 4096 1.0 -1.798 hbond; end "connect_atoms"; Matt On Jan 23, 2016, at 11:31 AM, Kubasik, Matthew A. <mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>> wrote: Bob and list, Are the energies used to color the h

Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

Bob, Could you expand on your comment that “Jmol uses typed arrays when possible"? I am in the habit of initializing arrays with a line like: a=array() Should I be doing something else? Does the array get “typed” after I add an entry? Matt On Dec 16, 2015, at 3:48 PM, Robert Hanson

Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

Daniel, Could it be the MO settings in your second file? The MO’s may be there, just hard to see. You may need to adjust the Jmol’s MO parameters in your second model that isn’t showing MO’s. MO documentation is here:

Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

tet i Tromsø - Norges Arktiske Universitet Norway Best regards also to the secret reader from the National Security Agency ____ Von: Kubasik, Matthew A. <mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>> Gesendet: Dienstag, 8. September 2

[Jmol-users] WebMO and Jmol Application

Bob and list, Like many others, I’ve been using WebMO to facilitate student access to computational engines on a server. Unfortunately, WebMO (on a desktop browser) still uses Java. Fortunately, WebMO easily facilitates running input files uploaded from a desktop. So, the plan is,

Re: [Jmol-users] WebMO and Jmol Application

Thank you, Bob, for your rapid fix. As to your question: yes, I am learning that there is almost nothing that Jmol cannot do! I’m not exactly sure what WebMO is doing, as installed on a computational server, so that it can receive/upload gaussian input files and run gaussian computations.

[Jmol-users] Feature Request: HPModes for Gaussian File Reader

Dear Bob, Could you and the Jmol development community consider adding the reading of “High Precision” modes (g09 option freq(HPModes)) to Jmol’s Gaussian file reader? Additionally, if the displacement vectors could be added to atom properties, that would be great! Currently, Jmol will reads

Re: [Jmol-users] Dissect PNGJ content?

the need and use for “true” in these additional split functions. I’ll play around with it and start a new thread when I get stuck. Matt On Aug 22, 2015, at 1:42 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: Am 22.08.15 um 17:23 schrieb Kubasik, Matthew A.: Thanks, Bob

Re: [Jmol-users] Dissect PNGJ content?

Thanks, Bob, for this. Can you clarify the purpose of “true”, as in: var x = load(“filename”, TRUE) I would like to learn when is it necessary. Your example uses “true” for .png but not for .cif. The help page shows the TRUE flag showing up elsewhere, as in the function x = y.split(,