Miguel,
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'?
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?
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?
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
--
|--------------------------------------------------|
| Dr Doug Chappell |
| Information Technology Officer, Computer Support |
| School of Molecular and Microbial Biosciences |
| The University of Sydney, 2006 NSW AUSTRALIA |
| [EMAIL PROTECTED] |
|--------------------------------------------------|
| Phone: 61 2 9351 2505 | Fax: 61 2 9351 4726 |
| 61 2 9351 2499 | |
|--------------------------------------------------|
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