select within(sequence,"ACGC")
selectionHalos on
You can also select for basepairs, and you can do some very sophisticated
searches for connectivity using Jmol bioSMARTS such as wild cards, variable
length subsets, etc. But for something that simple, SEQUENCE is best.
On Fri, Oct 14, 2011 at 12:05 PM, Moon Cheung <[email protected]> wrote:
> 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
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> 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
>> _______________________________________________
>> Jmol-developers mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> 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
> _______________________________________________
> Jmol-developers mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
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
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
