Thanks all guys!
I achieve it by writing a simple c program.my idea is to generate a script
file and run it by Jmol.
But i face another problem now.Can i highlight DNA sequence in Jmol?
For example, i have a pdb file 1A1G(1A1G.pdb) and the structure is show
below:
>1A1G:A|PDBID|CHAIN|SEQUENCE
MERPYACPVESCDRRFSDSSNLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKR
HTKIHLRQKD
>1A1G:B|PDBID|CHAIN|SEQUENCE
AGCGTGGGCGT
>1A1G:C|PDBID|CHAIN|SEQUENCE
TACGCCCACGC
Can i only highlight "ACGC"(which is in Chain C)?
Thanks very much.
Best Regards
Moon
2011/10/14 Rolf Huehne <[email protected]>
> On 10/13/2011 04:53 PM, Moon Cheung wrote:
> > Thanks Angel!
> > Since i am only a beginner.I still studying how Jmol works for my need.
> > I try to search the Jmol script by Google.But only script that use in
> > Webpage.
> > Is it the same for writing a .exe program?
> > Thanks very much
> >
> If you want to start Jmol as application you have different possibilities.
>
> I am not sure if I have understood what you really need:
>
> 1) Always run a specific Jmol script when Jmol is started.
>
> 2) Run one of several different scripts when Jmol is started, depending
> on the specific purpose for which Jmol is started.
>
> 3) Run a specific script while Jmol is already running.
>
> For case 1:
> As far as I know Jmol looks for a default script file in the home
> directory of the user. Unfortunately I don't remember the name of this
> file.
>
> You could also create a shortcut icon and add command-line options
> there. The Jmol Wiki contains a section on the application explaining
> this (http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options
> ).
>
> For case 2:
> You could create different shortcut icons with different options for
> different purposes.
>
> For case 3:
> You could customize the Jmol popup menu and add entries for your
> specific scripts. The Jmol Wiki contains a section explaining this
> (http://wiki.jmol.org/index.php/Custom_Menus) and also an additional
> example section
> (http://wiki.jmol.org/index.php/Recycling_Corner#Custom_pop-up_menus).
>
> Regards,
> Rolf
>
>
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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