Angel,

Thanks for all that.


> 3. How to pass args into a script from the command line ?

I meant command line args:†
java †-jar Jmol.jar †arg1 †arg2=val2 †etc


> 5. Can I do upper/lower case conversion of a string in Jmol ?

This was meant to simplify using a variable type of image file ..
(script setup at top)
suffix = "png" ; imagetype = "PNG";†
(later in script)
imagename = something + suffix;
write image @imagetype @imagename;

But as you say, the token PNG can be given to the "write" command as png. Problem solved. Good lesson. Things in UPPERCASE in the doco don't need to be.


> 6. Is there a compact reference for just the programming language of Jmol.
> you could create a documentation page (or rather an index with†pointers to the Scripting Doc sections) in the Wiki.
When I am more expert I might do that ! The reason for the question was, I sense that Jmol script started as 99% modelling commands (from RasMol and Chime) and simple scripting abilities, and then more complex language elements (loops, if/then/else, switch, more data types, etc) were added. Hence the doco is oriented around the modelling commands with the "programming" syntax a secondary thing. A strange ordering for a programmer (me) who is working with Perl, Python, JavaScript and sees the world (and Jmol) as a programming language with modeling commands added. :=)

Thanks again.


On 30 August 2013 18:38, Angel HerrŠez <angel.herraez@uah.es> wrote:
Hi Greg, and welcome!

> 1. Where is the doco of label parameters %a %n etc.

You got to the "label" doc,
http://chemapps.stolaf.edu/jmol/docs/#label
and it says "See atom properties for a detailed list of atom properties that
can be included in labels"
which leads you to
http://chemapps.stolaf.edu/jmol/docs/#atomproperties
The table there has both new and old syntax,
label %[xxx] † †label %x


> 2. I can open the console automatically from a script with "console". Can I size and place it ?
> Mainly to get it off the main render window.
If you are running the Jmol app, both its window and the console window
open at the last used position on screen (but I use Windows, not Mac)
For the applet, I don't think it can be done.


> 3. How to pass args into a script from the command line ? I think I have read it is not possible.
> _arguments are the args into a sub-script. Can args be passed via environment variables or a
> control file ?

Not sure about "arguments". You can pass script commands or load script
files, see
http://wiki.jmol.org/index.php/Jmol_Application#Loading_files_and_running_s
cripts

For the app, there is also "macros" from the top bar menu, which loads files.

What kind of arguments you speak about, and where would they be written?


> 4. Can I create a directory in Jmol script ?

Don't think so.


> 5. Can I do upper/lower case conversion of a string in Jmol ?

Don't know, please check Jmol Math doc. But I doubt it. What for?
Jmol scripting language is case-insensitive.


> 6. Is there a compact reference for just the programming language of Jmol. It seems scattered
> around in places like ..
> http://chemapps.stolaf.edu/jmol/docs/#jmolmath
> http://chemapps.stolaf.edu/jmol/docs/#while

Not sure what you'd call "programming". In some sense, all scripting is such.
Then you have the Jmol Math and the control structures as you have found.
What would you include under "programming language"? If you think it
relevant, you could create a documentation page (or rather an index with
pointers to the Scripting Doc sections) in the Wiki.


> Many thanks, aplogies for the newbie stuff.

That's Ok, that's why we have this list for

Good luck!


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--
Greg Edwards,
Port Jackson Bioinformatics
gedwards2@gmail.com