Doug CHAPPELL wrote:
I rarely used the RasMol commandMiguel,
Thanks very much for your interest - I have pasted some comments from the academic in charge of the course in answer to your queries below.
On Sun, Mar 13, 2005 at 11:25:29PM -0500, Miguel wrote:
In Molecular and Microbial Biosciences we currently use rasmol for a 4
hour
prac session. We would like to switch to jmol, however, the students save
the molecule state using the rasmol write script command. This allows
them
to submit material for assessment and also have their work reviewed by
demonstrators for guidance before they have finished the assignment. Is
the write script command likely to be implimented in the near future?
It is not on the list of things to be implemented in the short term ... but I am willing to talk about it.
I am not that familiar with the 'write script' command. My understanding is that it generates a large amount of data ... because it outputs attributes for each atom individually.
Q: Can you tell me a little more about your use of 'write script'?
write rasmol loadinlinescriptname.raz
only to get information about RasMol defaults, e.g. set ambient 40; set specular off
the output is not what I want to read e.g.
select (atomno>=140) and (atomno<=145)
spacefill 100
select (atomno>=358) and (atomno<=363)
spacefill 100
...
a history dump which may dump defaults and loaded scripts too, may be of more use
# java -Duser.language=en -jar Jmol.jar --script thisjmolscriptname.JMZ
# generated by Jmol Version 10.00.11 2005/03/13 17:34
# defaults
zap
English # this RasMol command which switches the application to English (French, Italian, Spanish) is not jet implemented in Jmol
...
# console input
load pdb http://....
# result of mouse interactions, this would be very interesting and superior to existing :-)
moveto ...
select ...
measure ...
# console input ...
# Tool script measure, :-) measure 995 1000
# Display script select carbon cpk 15%
# console input color green
# write jmol thisjmolscriptname.JMZ
This including mouse (in summary until the next interface ore console interaction) and interface actions would be superior over editing a script by hand and doing a
script myeditfile.JMZ
every time to restart view generation.
(Meanwhile an jmol.properties file for SciTe would be nice)
Students often need to return to their pictures to modify them and update
them. If they save them as images they can no longer reload them into Jmol
and change them. The script command in RasMol is used for this purpose.
One approach might be to save the whole series of commands line entries
(and pull down equivalents) as text after loading any pdb and writing it to
a text file as the picture is created.
So before loading you active the write script option on a pull down. As you
load you will be asked for the filename to dump the command txt into and
when you zap or exit the file will be closed.
Q: How large are the molecules you typically use?
protein with focus on sites
They view proteins upto 400 aa but generally not full atom representations. In more complex pictures they view the active sites of enzymes and include hbonds and Van der Waals contacts.
Q: Do others have experience with and/or comments about this?
history recording in InsightII Regards, Jan
I have heard of others using this feature of rasmol in a similar fashion - it would be interesting to see what others on the list have to say.
Thanks,
Doug
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