Hi Bob,
Thanks for the tip about the sticks representation. I tried running
compare 0 {1.1} {2.1} SUBSET LG1 ROTATE TRANSLATE
which resulted in NaN however
compare {1.1} {2.1} SUBSET LG1 ROTATE TRANSLATE 0
seems to work beautifully.
However, the alignment of the LG1 residue (it is a ligand defined as one
residue with HETATM records) does not seem to work as well as PyMOL. In
PyMOL, the ligands overlap perfectly but using the compare command above,
they align close but incorrectly. This is probably something I am doing
wrong. I did notice that the order of the atoms in LG1 is different between
1.1 and 2.1. The residue number is also different in both models although
there is only one LG1 residue in each model. The PyMOL command I am trying
to replicate is:
select design_ligand, Design and resn LG1
select template_ligand, Template and resn LG1
pair_fit template_ligand, design_ligand
where 1.1 is the template in JSmol and 2.1 is the design.
A PSE reader would be great for us since we already have all the PSE files
generated. I did try loading one last week (2.4MB in size) but I just got
an empty canvas. I can check to see whether I would be allowed to send you
the file if you are interested in debugging it. In terms of participating
with your work on the reader, I am not sure how I could contribute. I could
certainly test to see whether our PSE files work. Please feel free to send
me a direct email if you can think of any way I could help.
Regards,
Shane
On Thu, Apr 4, 2013 at 3:11 PM, Robert Hanson <[email protected]> wrote:
> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> Employer Resources Portal
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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
> Employer Resources Portal
> http://www.cisco.com/web/learning/employer_resources/index.html
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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