PS, Jaime Prilusky and I are madly working on a PyMOL PSE file reader, in
case you are interested in that. I would say we are 80% there -- all the
simple things are working; some issues, of course; not ready for full
release, but every day is better. Care to participate?
Bob
On Thu, Apr 4, 2013 at 4:52 PM, Robert Hanson <[email protected]> wrote:
>
>
>
> On Thu, Apr 4, 2013 at 1:43 PM, Shane Ó Conchúir <[email protected]>wrote:
>
>> Hi all,
>>
>> I am currently trying to rewrite a PyMOL script in JSmol and hitting a
>> problem after the first JSmol compare command.
>>
>> The PyMOL script is:
>>
>> select design_ligand, Design and resn LG1
>> show sticks, design_ligand
>> select template_ligand, Template and resn LG1
>> pair_fit template_ligand, design_ligand
>> super Scaffold, Design
>> # I'm not sure what the original author intended here
>> hide lines, Scaffold
>> hide ribbon, Scaffold
>> show car, Scaffold
>> util.cbc Scaffold
>> disable Scaffold
>>
>> and I am trying to mimic this with this JSmol script (I may have gotten
>> some of the translation wrong):
>>
>>
>
>> select LG1:X/2;
>>
>
> wireframe -0.1 // more like PyMOL sticks; the "-" indicates "turn
> everything else off"
>
>
>
>> wireframe only; wireframe reset; spacefill reset; // select
>> design_ligand, Design and resn LG1; show sticks, design_ligand
>> compare {1.1} {2.1} SUBSET LG1 ROTATE TRANSLATE; // select
>> template_ligand, Template and resn LG1; pair_fit template_ligand,
>> design_ligand
>> compare {3.1} {2.1} ROTATE TRANSLATE; // super Scaffold, Design
>> select 3.1; cartoon only; color chain; hide 3.1; // hide lines,
>> Scaffold; hide ribbon, Scaffold; show car, Scaffold; util.cbc
>> Scaffold; disable Scaffold
>>
>> The JSmol lines above (without the comments) are stored in an array and I
>> loop through the array calling the Jmol.script function on each line. The
>> problem is that the first 'compare' command starts an alignment animation
>> which takes a few seconds and the last line which hides model 3 does not
>> seem to run. If I pop open a console and run the command manually after the
>> animation completes, 3.1 is hidden as expected.
>>
>
> You can add a time for the compare to be 0, and it will execute
> immediately:
>
> compare 0 {1.1}......
>
> Ah, I see that didn't get documented.....
>
> Bob
>
>
>
>>
>> Should I do something to wait until the animation stops before
>> calling Jmol.script again? If so, is there any state function that lets me
>> know that it is okay to start executing commands?
>>
>> Regards,
>> Shane
>>
>>
>> ------------------------------------------------------------------------------
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>> _______________________________________________
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>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
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http://www.cisco.com/web/learning/employer_resources/index.html
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