Difference between revisions of "Borrowed JSmol"
AngelHerraez (talk | contribs) (Borrowed JSmol) |
AngelHerraez (talk | contribs) (Borrowed JSmol) |
||
| Line 2: | Line 2: | ||
== Display using JSmol of structures uploaded to a cloud service == | == Display using JSmol of structures uploaded to a cloud service == | ||
| − | There are 2 | + | There are 2 components in this approach: |
| − | * where the | + | * where to locate the webpage that embeds the JSmol object (a common resource), |
| − | * where the file with the molecule or structure | + | * where to locate the file with the molecule or structure (your personal file) |
:''An idea picked from'' [http://molecularmodelingbasics.blogspot.com.es/2015/11/quick-way-to-share-interactive.html Quick way to share interactive molecular structures and animations] by Jan Jensen (licensed under Creative Commons Attribution 4.0) | :''An idea picked from'' [http://molecularmodelingbasics.blogspot.com.es/2015/11/quick-way-to-share-interactive.html Quick way to share interactive molecular structures and animations] by Jan Jensen (licensed under Creative Commons Attribution 4.0) | ||
| Line 11: | Line 11: | ||
Display of the molecular structure in a JSmol panel is achieved via this page provided by Bob Hanson: | Display of the molecular structure in a JSmol panel is achieved via this page provided by Bob Hanson: | ||
{{StOlaf}}jmol.php | {{StOlaf}}jmol.php | ||
| − | with a special syntax in the URL | + | with a special syntax in the URL, i.e. you must append the <code>?source=</code> token followed by the url of your molecular file (see examples below). |
The URL may easily be copied and shared by email, Tweet, blog or any other means to whoever you want to show your molecular model to. Since all data are in public servers and the page uses JSmol/html5, it is most likely that ayone can view it on any platform, without installing or learning any software. | The URL may easily be copied and shared by email, Tweet, blog or any other means to whoever you want to show your molecular model to. Since all data are in public servers and the page uses JSmol/html5, it is most likely that ayone can view it on any platform, without installing or learning any software. | ||
| Line 54: | Line 54: | ||
=== Other servers === | === Other servers === | ||
| − | It may also be possible to use any other web server, as long as you can grab a permanent url that directly points to your file. | + | It may also be possible to use any other web or file server, as long as you can grab a permanent url that directly points to your file. |
=== Custom displays via script === | === Custom displays via script === | ||
| − | The idea is to link to a JmolScript file rather than to the molecular file. In this way, you provide a personalized view and rendering, or | + | The idea is to link to a JmolScript file rather than to the molecular file. In this way, you provide a personalized view and rendering, activate spin or vibration or animation,... without any further instructions for your target colleague to operate JSmol. |
Remember that the script file must contain a load command that points to the url of the molecular file. | Remember that the script file must contain a load command that points to the url of the molecular file. | ||
| − | Another possible solution is to save a PNG+JMOL file, upload it and then serve that to the StOlaf | + | Another possible solution is to save a PNG+JMOL file, upload it and then serve that to the StOlaf jmol.php page. That should preserve the whole state of the model. |
| − | |||
| − | |||
== Hosting JSmol pages in a cloud service == | == Hosting JSmol pages in a cloud service == | ||
''...pending...'' | ''...pending...'' | ||
Revision as of 19:06, 18 December 2015
This page collects methods for displaying structures in JSmol on the web without actually having control of a web server.
Contents
Display using JSmol of structures uploaded to a cloud service
There are 2 components in this approach:
- where to locate the webpage that embeds the JSmol object (a common resource),
- where to locate the file with the molecule or structure (your personal file)
- An idea picked from Quick way to share interactive molecular structures and animations by Jan Jensen (licensed under Creative Commons Attribution 4.0)
JSmol display
Display of the molecular structure in a JSmol panel is achieved via this page provided by Bob Hanson:
https://chemapps.stolaf.edu/jmol/jmol.php
with a special syntax in the URL, i.e. you must append the ?source= token followed by the url of your molecular file (see examples below).
The URL may easily be copied and shared by email, Tweet, blog or any other means to whoever you want to show your molecular model to. Since all data are in public servers and the page uses JSmol/html5, it is most likely that ayone can view it on any platform, without installing or learning any software.
If you want to share a customized view of your molecule (not just the default ball & stick rendering), the way to follow is to write a small script file that will load the molecule and then apply any Jmol scripting. Then your link should use the url of that script file rather than the molecular file. See details below.
Once your molecular file has been uploaded to figshare, copy the link to it (it may be in any file format that Jmol accepts, like the most common pdb and mol formats).
For example:
| link to file | http://files.figshare.com/1860026/ethen_01oIRC.cml |
|---|---|
| url for JSmol display | https://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1860026/ethen_01oIRC.cml |
- (Thanks to @janhjensen for the tip)
DropBox
Once your molecular file has been uploaded to Dropbox, you need to trick the regular link, of the form
https://www.dropbox.com/s/xxx/file?dl=0
changing it to this form:
http://dl.dropboxusercontent.com/s/xxx/file
and then append it to the JSmol url:
- (Thanks to @janhjensen and @aminophen for the tip)
Other servers
It may also be possible to use any other web or file server, as long as you can grab a permanent url that directly points to your file.
Custom displays via script
The idea is to link to a JmolScript file rather than to the molecular file. In this way, you provide a personalized view and rendering, activate spin or vibration or animation,... without any further instructions for your target colleague to operate JSmol.
Remember that the script file must contain a load command that points to the url of the molecular file.
Another possible solution is to save a PNG+JMOL file, upload it and then serve that to the StOlaf jmol.php page. That should preserve the whole state of the model.
Hosting JSmol pages in a cloud service
...pending...
