[Jmol-users] [n = {*}[0].molecule;show n] bug

Bob, First, AAARGH! Finally. Here’s what messes up [n = {*}[0].molecule;show n] in Jmol - Otis.htm and Test2.htm PubChem provides SDF's with partial charges and without partial charges. Actually, they are always there, but some are listed > 0 If the PubChem file actually lists non-zero cha

Re: [Jmol-users] RCSB

Ouch!! On Tue, Jun 28, 2016 at 4:49 PM, Otis Rothenberger wrote: > Phil, > > In my attempt to locate my [n={*}[0].molecule;show n] problem mentioned in > a previous email, I downloaded today’s version. I can confirm pdb load > problem. The console says the pdb is loaded, but nothing is visible.

Re: [Jmol-users] page-developer request - Jmol Unplugged

Bob, For the past year, I have working to make the model kit self contained. To do this, I am detecting 3 states: 1) On-line and served. 2) On-line and local. 3) Local only. The code automatically detects these states and does 3 things (item numbers below ref above item numbers): 1) Good to g

Re: [Jmol-users] page-developer request - Jmol Unplugged

Bob: Here is a link to a directory that contains stereochemistry and spectroscopy tutorials which our students have found helpful. It is small and runs without network connection. The index file contains the links to the two sets of tutorials, or you can just open them from the appropriately t

Re: [Jmol-users] RCSB

Phil, In my attempt to locate my [n={*}[0].molecule;show n] problem mentioned in a previous email, I downloaded today’s version. I can confirm pdb load problem. The console says the pdb is loaded, but nothing is visible. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun

Re: [Jmol-users] page-developer request - Jmol Unplugged

Dear Bob I will likely get involved on this. For now, just two quick comments that popped up: 1. I have had big trouble running my pages locally since I moved to JSmol. That may be due to them being old and ellaborate, with a combination of folders, pdb or mol files, scripts, common JS files.

Re: [Jmol-users] resolution of JPG images

Hi Rick a few comments: 1. I can recommend that you try PovRay output. It is PNG, transparent background and much better look. You don't need to learn how to use PovRay, producing the images is straightforward. You have to install PovRay, export to PovRay format from Jmol and then save from Pov

[Jmol-users] RCSB

In today’s version (…..6.28) the RCSB protein files in jsmol.htm do not load correctly. Yesterday’s version (….6.27) worked. Can anyone else confirm that? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu --

Re: [Jmol-users] resolution of JPG images

Rick, the first thing you should do is contact your publisher and make absolutely certain they cannot accept PNG images. In all cases PNG images are better than JPG because they are "lossless". JPG images notoriously have artifact pixels that are not part of the actual image. I don't think the 72-p

Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

Otis, this is because your site is doing something funky. Or there's a bug. {*}[0] is an atom reference, not a number. It has all the properties of an atom, including .molecule. ​ -- Attend Shape: An AT&T Tech Expo July

[Jmol-users] page-developer request - Jmol Unplugged

Jmol page developers, Today I am giving a workshop on the use of Jmol in general and inorganic chemistry. Tomorrow the subject is organic chemistry, and Thursday it is physical chemistry. These workshops are at the Universidad Mayor San Simón, in Cochabama, Bolivia. Please feel free to come and he

Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

Bob, > > {*}[0] > Agree: It appears to generate the atomIndex of the last atom. > {*}[0].molecule > I don’t think so: It consistently generates the number 1 for any number of fragments in the window. On the other hand, using the infinite number of monkeys writing Shakespeare approach, n

[Jmol-users] resolution of JPG images

I am trying to produce some high quality images for publication and would like to use JSmol, however it seems that the resolution is set at 72 dpi and cannot be changed. It is possible to make this a variable the user can set? Also (for the wish list) any chance of getting a vector format such a

Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

On Tue, Jun 28, 2016 at 1:24 AM, Otis Rothenberger wrote: > Bob, > > My model kit puts multiple models in the same Jmol frame. It appears that n > = {*}.molecule[0] (not n = {*}[0].molecule) is the correct expression, > but results are very erratic. The value of n is often (but not always) 2X > t

[Jmol-users] Download Jmol-14.6.0_2016.06.28-binary.zip (66.5 MB)

Jmol.___JmolVersion="14.6.0_2016.06.28" bug fix: using an exporter (write VRML, eg) with cartoonsFancy will break rendering after that bug fix: after loading PNGJ data, using write FILE crashes Jmol * Download Jmol-14.6.0_2016.06.28-binary.zip (66.5 MB)