Re: [Jmol-users] reordering IRC frames and pasting two halves together

Gaussian missing energy -- that should be fixed for http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.19b.zip (uploading now). Please let me know if it is not. should be print getProperty("modeInfo.models[1].energy") for example, or from JavaScript: var e = Jmol.evaluate(jmolApplet0, 'ge

Re: [Jmol-users] reordering IRC frames and pasting two halves together

On Mon, Aug 19, 2013 at 9:37 PM, Whitwell, George wrote: > Thanks, Bob. > > > > REVERSEMODELS works as advertised. I have to load the first file reversed > - they both start at the saddle point. > > > > I tried getproperty modelinfo.models.energy to retrieve the energies. I > get back "" for al

Re: [Jmol-users] reordering IRC frames and pasting two halves together

Thanks, Bob. REVERSEMODELS works as advertised. I have to load the first file reversed - they both start at the saddle point. I tried getproperty modelinfo.models.energy to retrieve the energies. I get back "" for all my 57 frames, so I think that these values may not be extracted from t

Re: [Jmol-users] new Jmol feature: rotate BEST

Sure. rotate BEST does more than simple 90-degree rotations. Could be different definitions of what is "best" of course. What it has now is "smallest volume with thinnest side directed toward the user and longest side along X." Were you sure to select the same set of atoms as you did in your al

Re: [Jmol-users] new Jmol feature: rotate BEST

Am 19.08.2013 23:55, schrieb Robert Hanson: > What's your algorithm for that, Rolf? > The idea is to bring the largest boundbox plane to the front. So first the x,y and z boundbox vector length is determined. Then for each possible case the required rotations are done. Since I developed the algori

Re: [Jmol-users] reordering IRC frames and pasting two halves together

For the second one, use: load append .gamess filter "REVERSEMODELS" has worked in the past for me, at least for Spartan files. After that, you might have to delete one or more models. You also may need to do some alignment. For that see http://chemapps.stolaf.edu/jmol/docs/index.htm?search=

Re: [Jmol-users] new Jmol feature: rotate BEST

What's your algorithm for that, Rolf? -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Mo

[Jmol-users] reordering IRC frames and pasting two halves together

Hi, I have GAMESS output from both sides of the reaction coordinates from a Cl-CH3-Br anion intermediate as an example of an SN2 reaction. I can load both output files in Jmol as different models and animate them consecutively; however, since they both run downhill, it isn't really the sequenc

Re: [Jmol-users] new Jmol feature: rotate BEST

On 08/19/2013 01:19 PM, Rolf Huehne wrote: > On 08/19/2013 02:10 AM, Robert Hanson wrote: >> For example, your database shows structures. What's the best default >> orientation to show such that the longest side of the box is along X and >> the shortest depth is toward the user? >> >> rotate BEST >

Re: [Jmol-users] Fwd: Getting data back from jmol command line

Perfect - didn't realize it would be so easy :) Sincerely, James Ryley, PhD, Patent Agent SumoBrain: Intellectual Property Solutions & Data AcclaimIP | FreePatentsOnline.com| SumoBrain.com | BioMedSearch.co

Re: [Jmol-users] new Jmol feature: rotate BEST

On 08/19/2013 01:19 PM, Rolf Huehne wrote: > On 08/19/2013 02:10 AM, Robert Hanson wrote: >> For example, your database shows structures. What's the best default >> orientation to show such that the longest side of the box is along X and >> the shortest depth is toward the user? >> >> rotate BEST >

Re: [Jmol-users] new Jmol feature: rotate BEST

On 08/19/2013 02:10 AM, Robert Hanson wrote: > For example, your database shows structures. What's the best default > orientation to show such that the longest side of the box is along X and > the shortest depth is toward the user? > > rotate BEST > I thought that this might be an intended usage. B