Re: [Jmol-users] unloading molecule

[Rolf H. <rh...@fl...>]

Zeyar Aung wrote:
> Hi All,
>  
> What is the Jmol script command to unload a molecule that is currently in display?
>  
The command is "zap". But this is automatically done if you load a new
structure with 'load "filename"'. Only if you use the "APPEND" keyword
within the load command the file is loaded additionally and no 'zap' is
done.

> And what is the script command to quit Jmol?
>
There is no script command to quit Jmol (as far as I know). For batch
processing purposes like you describe it below there is the command-line
switch "-x" which will make Jmol exit automatically after the script
(provided after the command-line switch "-s") is finished.

> I have looked into Jmol documentation (http://chemapps.stolaf.edu/jmol/docs/ <http://chemapps.stolaf.edu/jmol/docs/> ) but could not find the answers.
>  
The documentation on command-line switches available here
(http://jmol.sourceforge.net/docs/JmolUserGuide/ch02.html) is
unfortunately not up-to-date.
It might be a good idea to include the command-line options also into
the Jmol scripting documentation because they are relevant for batch
scripting and would therefore also fit in there.

You can get an overview on the current command-line options by starting
the application with the "-h"/"--help" switch:

  java -jar Jmol.jar -h

======= Help Output ===============
usage: Jmol
 -o,--noconsole               no console -- all output to sysout
 -q,--quality                 JPG image quality (1-100; default 75) or PNG
                              image compression (0-9; default 2, maximum
compression 9)
 -g,--geometry                window width x height, e.g. -g500x500
 -x,--exit                    exit after script (implicit with -n)
 -D <property=value>          supported options are given below
 -b,--backgroundtransparent   transparent background
 -c,--check                   check script syntax only
 -h,--help                    give this help page
 -i,--silent                  silent startup operation
 -l,--list                    list commands during script execution
 -m,--menu                    menu file to use
 -n,--nodisplay               no display (and also exit when done)
 -s,--script                  script file to execute
 -t,--threaded                independent commmand thread
 -w,--write                   CLIP or GIF|JPG|JPG64|PNG|PPM:filename

For example:

Jmol -ions myscript.spt -w JPEG:myfile.jpg > output.txt
======== End of help output (not shown completely here) ========

> What I am trying to do is to write a script file to load a protein, do some visual modifications, save it as an image file, unload it, and the load another protein, and so on. I have hundreds of protein to be processed in this way. After processing them all, I would like to quit Jmol automatically.
>
I am doing something similar to what you describe for all PDB entries
(asymmetric and biological units). This means generating about 100,000
images automatically with Jmol.

My first approach was also to generate a single script that contains
load structure and write image commands for all entries (or a couple of
thousands for parallel processing in a multiprocessor system).
But this has several disadvantages:

1) It takes a very long time until processing of the script starts. With
several thousands line of Jmol script it took about an hour (as far as I
remember). It seems like Jmol is first parsing the whole script
(unexpectedly slowly). So if anything goes wrong it will take quite a
while until you can notice it.

2) If there occurs an error somewhere within the script, the rest of the
script is not executed. So if you are unlucky and there is a problem
with file number 10 then you don't get images for the remaining 90 files
in your list.

3) It is more difficult to check if everything was generated properly.

Therefore I switched to a different approach: starting Jmol for each
file individually. This has several advantages:

1) Processing starts immediately.

2) If there is a problem with file number 10 you will have 99 images in
the end (instead of 9 with the other method). And you just have to
handle the one problematic case.

3) It is much easier to check for processing errors. In my case there
ocurred sometimes non-reproducible errors in generating the image. This
means that there were no problems with the same PDB entry in a different
run or doing the same manually. So now I immediately check if there was
generated an image and if it looks right (by comparing it with an empty
image of the same size, because the main error was that the generated
image was empty). If not I redo the same up to 3 times. This reduced the
failure rate considerably.

I would also recommend to use the "-o" switch. This will enable you to
capture all error mesages and also other messages for error checking or
capturing information printed by the script.

If there are further questions, don't hesitate to ask them.

Regards,
Rolf