Thanks, Egon. Somehow that got on the users list. Did you intend that? Seems
like a Jmol-developer concept, so I've switched to that. Comments below.
Egon Willighagen wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> On Monday 27 September 2004 18:01, Bob Hanson wrote:
>>I also checked out Jmol-web and CVSROOT, so I think I now have pretty
>>much the whole thing.
> CVSROOT is not something you need to have a look at. It contains stuff
> enabling CVS commands to be tracked... e.g. there are scripts that will
> ensure that the CVS commits gets loged to the jmol-commits@ mailing list,
> which I can recommend to subscribe to, and loged to the #cdk IRC chat channel
> on the irc.freenode.net network, where CDK developers get together (and
> Miguel too in the past, but not lately...)
Right, I see that now. Interesting, but not something I would ever deal with
directly. I see that it's all unused except checkoutlist, ciabot_cvs, loginfo,
and syncmail. That makes sense. What a slick system.
>>OK, let's talk a bit about how/where you see the documentation fitting
>>in. I think I need to incorporate your header in there, for example.
> Yes, it would need a header with some information: license, and some CVS
> tracking info. E.g.:
> /* $RCSfile: JmolApplet.java,v $
> * $Author: migueljmol $
> * $Date: 2004/07/30 11:50:57 $
> * $Revision: 1.89 $
> * ... etc
> The $RCSfile: $ etc. gets updated whenever you do a commit.
I see. The keywords $RCSfile $Author $Date $Revision define fields that will be
updated. What's the ",v" in $RCSfile? Or don't I worry about that, because these
will be updated automatically? I presume that if this information is not
present, then that's OK (I see it isn't in every .js file, for example). But it
makes sense for me to put it in. I notice that it also isn't in the xml files in
the Jmol-web/doc/source area.
>>Is there a specific directory that this needs to go into? Basically it's
>>a couple of .htm files and .js files in a main directory and a set of
>>examples in a subdirectory. In addition, there is a .xls file that
>>generates all the code.
> I assume that it's quite standalone, but will get placed on http://www.jmol.org. The
> Jmol-web modules might apply, but am not sure if it would conflict with the
> current dir structure... Miguel?
subdirectories for topics; no obvious introductory or explanatory HTML
this seems the logical place to introduce this as a fourth resource.
OK, I'm catching on. I haven't used XML before, but this is slick.
I can see right now that
needs some updating. (I'm not volunteering.)
Q: What provision is in place to allow this site to be house-tested prior to
going "live" with users?
>>Also, am I right that "codebase" can't refer to "../../applet" that is,
>>two levels up and one over? When I tried that I got an error.
>>How on the project site are you maintaining reference all to the same
> When on http://www.jmol.org we have the option to say something like
> codebase="/jmol/Jmol.jar" which would point to http://www.jmol.org/jmol/Jmol.jar
> But ../ in codebase="" should work too, see
I see how [codebase] is working:
<applet name="anim" code="JmolApplet" archive="JmolApplet.jar"
width="350" height="350" mayscript="true">
<param name="load" value="SN1_reaction.xyz">
does the trick. This is getting integrated using build.xml
I also see in build.xml how that gets replaced differently depending upon the
location of the file. Fabulous.
I'm curious where http://jmol.sourceforge.net/jmol/ comes from, as I don't see
it under Jmol-web. Oh, wait. I see. It's created in the build. OK. It looks to
me like the demos in
are using their own private version. Hmm:
JmolApplet.jar 21-Sep-2004 13:24 620k
JmolApplet.properties 21-Sep-2004 13:24 1k
Jmol.js 21-Sep-2004 13:23 17k
JmolApplet.jar 21-Sep-2004 13:23 516k
How do you explain the two different file sizes?
Created just a minute apart?
OK, so I presume the demo pages are using their own applet. Maybe there's a
reason for this.... I'd rather just use the main applet.
Is that because you can't use the relative reference ../../jmol/ as a codebase
in demo/aminoacids ?
Is this the way it should be?
I suggest that I compose the page as XML within the /demo/ directory. (Do you
just do this by hand, or do you have an XML writer? It would be good for me to
do it by hand. I'll learn XML. I realize I have to be far more careful with my
tags and such. Most of it is in .js files, anyway. But it would be interesting
to code the example pages as XML. That might be a later project.)
What are people's feelings about the demos currently in /demo/? Should I try to
integrate them into the documentation somehow?
Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057