Quick way to share interactive molecular structures and animations

#compchem http://t.co/tWJweuf1wF look at this dehydration. Right click on white space, press animation mode 'loop', right click and play

— gyges01 (@gyges01) October 16, 2015

Here is a neat trick I learned from @gyges01 on Twitter.  Say you want to share an interactive molecular structure or animation with someone not well versed in structural visualization tools. Here's what you do.

1. Put your file on a server like figshare and copy the link. For example: http://files.figshare.com/1860026/ethen_01oIRC.cml
Unfortunately, a dropbox link, which would have been even easier, does not seem to work. See below

2. Combine this link with "http://chemapps.stolaf.edu/jmol/jmol.php?source=":
http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1860026/ethen_01oIRC.cml

3. Email (or Tweet) the link (takes a minute to load) with instructions to start animation: right-click > animation > play

4. You can autostart the animation by uploading a "dummy" xyz file with the commands: http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/2367420/ethen_test.xyz

ethen_test.xyz looks like this:

1
jmolscript: load http://files.figshare.com/1860026/ethen_01oIRC.cml; animation on; animation mode palindrome;
h 0.0 0.0 0.0

@janhjensen Amazing! And I found Dropbox link is also available! Two keys are: http (not https), and https://t.co/TImsktm2Fx

— Acetaminophen (@aminophen) November 23, 2015

2015.11.23 Update Twitter strikes again: @aminophen found the trick to making this work with Dropbox.  Change https://www.dropbox.com/s/xxx/file?dl=0 to http://dl.dropboxusercontent.com/s/xxx/file.  Example:
https://www.dropbox.com/s/t42dx22mxsioja6/ethen_test.xyz?dl=0 to http://dl.dropboxusercontent.com/s/t42dx22mxsioja6/ethen_test.xyz and use it like before: http://chemapps.stolaf.edu/jmol/jmol.php?source=http://dl.dropboxusercontent.com/s/t42dx22mxsioja6/ethen_test.xyz



This work is licensed under a Creative Commons Attribution 4.0

Computational Chemistry Highlights: October issue

The October issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, David Bowler and Jan Jensen:

Stochastic Multiconfigurational Self-Consistent Field Theory

Unusual H-Bond Topology and Bifurcated H-bonds in the 2-Fluoroethanol Trimer

Benchmarking Continuum Solvent Models for Keto–Enol Tautomerizations

Mechanism of the Intramolecular Hexadehydro-Diels–Alder Reaction

The accuracy of semi-local functionals

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This work is licensed under a Creative Commons Attribution 4.0