Re: [Jmol-users] Newbie question: showing a docked receptor-ligand model (applet)

[<ari...@cb...>]

Thank you very mucho for your help!

> The difficulty is defining the atoms involved in the receptor...showing
> bonds and ribbons in the entire protein is quite easy:
>
> select protein; cartoon on;
>
> The ligand will display initially as bonds and atoms. I suspect this isn't
> what you want :-) Here's script for displaying bonds and atoms only
> within,
> say, 6 Angstroms of the ligand(s):
>
> select protein; cartoon only; select within(6.0,ligand);wireframe 60;
> spacefill 100;
>
> and if you're interested only in displaying sidechains:
>
> select protein; cartoon only; select within(6.0,ligand) and
> sidechain;wireframe 60; spacefill 100;
>
> You can save that script to a .spt file for easy retrieval elsewhere (and
> easy updating, if your fancy changes later), or you can just copy and
> paste
> it in the second argument of jmolApplet, just after "load
> 1.1_1.1_1__receptor.pdb."
>
> Cheers, Mike
>
> On Wed, Mar 2, 2011 at 10:17 AM, <ari...@cb...> wrote:
>
>> Hello, i would like to find examples about how to define default values
>> for a receptor-ligand model (pdb format).
>>
>> <script>
>>            jmolApplet(400, "load 1.1_1.1_1__receptor.pdb");
>> </script>
>>
>> For us is useful to load the applet showing "ribbons" and "bonds" for
>> the
>> receptor and "bonds" only for the ligand.
>>
>> Are any available Jmol example settings with receptor-ligand models?
>> Thank you.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Free Software Download: Index, Search & Analyze Logs and other IT data
>> in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT
>> data
>> generated by your applications, servers and devices whether physical,
>> virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> Jmol-users mailing list
>> Jmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Mike Evans
> Organic Chemistry Graduate Student
> Moore Group
> University of Illinois, Urbana-Champaign
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT
> data
> generated by your applications, servers and devices whether physical,
> virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>