[Molvis-list] Script for saving files in Chime

Eric Martz emartz at microbio.umass.edu
Tue Jan 4 16:42:19 EST 2005

At 12/28/04, you wrote:
>Dear colleagues,
>   We are working on a Chime based project that requires loading a molecule
>from the hard disk, manipulating its coordinates by an external code and
>saving the new structure.  We would like to know if there is a way to
>control Chime's "Save Molecule As" function through the Chime script.  We
>want to have a button on our Website which, using JavaScript and Chime's
>script, will open the "Save Molecule As" dialog box and enable the user to
>save the current molecule to his/her hard disk. We know it is possible in
>Rasmol.  Is this possible in Chime?
>Best wishes,

Dear Inbal:

The "save" commands from RasMol were disabled for security reasons when the 
RasMol code was ported to Chime. The only PDB file save from Chime is via 
Chime's menu (click on MDL, File, Save Molecule As). This always saves the 
PDB file exactly as it was received, including the original header, and 
without any changes regardless of what is selected or rotations, etc. (see 
http://www.umass.edu/microbio/rasmol/pdbtools.htm). (Actually there is a 
bug in Chime -- sometimes it saves the most recent command script instead 
of the PDB file.)

So I don't think you can put a button in a web page that will initiate the 
save dialog with Chime, but you can simply explain how to use Chime's menu 
to do this (3 clicks instead of one).

It may be possible to do what you want with the Jmol applet. Can someone 
confirm and give details? Jmol is open-source and understands essentially 
all Chime script commands (except not yet surfaces). It comes from your 
server instead of the client having to install a plugin. It is already more 
flexible and powerful than Chime in most areas. www.jmol.org


Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US

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