Re: [Jmol-users] Jmol 14.13.1

Dean and Pshemak, First, OK I'm a believer. The command "display unitcell" is real, and it's neat. It cuts off all of the exterior atoms (to unit cell). That's good to know. On the desktop app issue, I think I was one of the early users to say good-bye to Java. I'm a small molecule guy, and

Re: [Jmol-users] Jmol 14.13.1

Thank you Dean, I do not understand the lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; part of the command. Is it documented in https://chemapps.stolaf.edu/jmol/docs/ ? Thanks, PM On 4/10/2017 10:46 AM, Dean Johnston wrote: Yes - I have an example at:

Re: [Jmol-users] Jmol 14.13.1

Thank you Dean, I do not understand the lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; part of the command. Is it documented in https://chemapps.stolaf.edu/jmol/docs/ ? Thanks, PM On 4/10/2017 10:46 AM, Dean Johnston wrote: Yes - I have an example at:

Re: [Jmol-users] Jmol 14.13.1

Pshemak, The CAP part is discussed here: https://chemapps.stolaf.edu/jmol/docs/index.htm?=1=14.6#isosurface Scroll down until you see CAP listing. The spacefill 1% is just hiding the atoms leaving the lcaocartoons Dean,

Re: [Jmol-users] Jmol 14.13.1

Otis and Dean,, Thanks for the explanation. I was indeed able to find the whole command (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off/) / in the documentation (in the "cpk" example of lcaoCartoons). I think I understand it better now. The "spacefill" spheres are

Re: [Jmol-users] Jmol 14.13.1

Pshemak, Otis and Bob, Glad that I could provide something to the list. I have to admit that I set that page up long enough ago that I can't recall exactly how I figured it out. But it still works and it's useful. Dean On Mon, Apr 10, 2017 at 3:09 PM, Robert Hanson wrote:

Re: [Jmol-users] Jmol 14.13.1

Otis and Dean, I just tested NaCl in JSmol (JavaSript) on a rather old version (14.4.1). Surprise: it works as intended (no freezing). I will do more testing. Otis, I will send you the cif files to your address (list does not allow attachments). Thanks, PM On 4/10/2017 1:49 PM, Otis

Re: [Jmol-users] Jmol 14.13.1

Pshemak, Gotta love this error message: java.lang.IllegalArgumentException: Comparison method violates its general contract! I'll check on this. Bob On Mon, Apr 10, 2017 at 12:21 PM, Pshemak Maslak wrote: > Otis and Dean,, > > Thanks for the explanation. I was indeed

Re: [Jmol-users] R: Re: Jmol 14.12.1 released -- R/S chirality

Il 09/04/2017 21:16, pinostricc...@alice.it ha scritto: Great job, Bob. Really. I will implement it on my website for my students to use. Sometime imagining molecules in 3D is not that easy :) @Pierluigi. I was referring to your pages too with my compliment Pino Messaggio originale

Re: [Jmol-users] Jmol 14.13.1

Pshemak and Dean, Back in the day, I was just an organic chemist who had to prove to my X-ray colleagues that my molecule was worthy of their efforts (data returned on punch cards). Consequently, I admit to a weak point explaining my tests below on Pshemak's file. But here goes: On both

Re: [Jmol-users] Jmol 14.13.1

OK, I know how I my comparison method violated the general contract. Very surprised this ever worked! On Mon, Apr 10, 2017 at 1:37 PM, Robert Hanson wrote: > Pshemak, > > Gotta love this error message: > > java.lang.IllegalArgumentException: Comparison method violates its >

Re: [Jmol-users] R: Re: Jmol 14.12.1 released -- R/S chirality

Many thanks, Pino! If you like it, my page is now online on the production site at: http://www.iorgchem.unito.it. The page is in the menu Esercizi ---> Esercitarsi sulla Chiralità. The page was now updated and the scope is to make students to follow the full path: 1) assign the labels to

Re: [Jmol-users] Jmol 14.13.1

Dear Bob, many thanks for the crucial update! Yesterday I have published on the site the page for the step-by-step chirality assignment procedure. It should be intended for compound having only one chiral carbon since I did not implemented yet any function to take into account the presence

Re: [Jmol-users] Jmol 14.13.1

Dear Bob, Sorry... I forgot to add the address of the production site: http://www.iorgchem.unito.it/index.php/en/exercises/practice-on-chirality bye! Pierluigi il 10/04/2017 04:44, Robert Hanson ha scritto: https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.13/Jmol%2014.13.1/

Re: [Jmol-users] Jmol 14.13.1

Can the "slab" command be used to produce presentations equivalent to the image linked below? https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg If so, any suggestions on how to do that would be appreciated. Thanks, PM

Re: [Jmol-users] Jmol 14.13.1

Yes - I have an example at: http://crystals.otterbein.edu/packing/index.html Pick structure from the left menu and then click the “Show Contents of One Unit Cell”. Works beautifully! The commands are: display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%;