[Chimera-users] Set interatomic distances

George Patargias gpat at bioacademy.gr
Mon Nov 18 23:36:01 PST 2013


Hello Elaine and Eric

Many thanks for your useful comments!

George

> Hi George,
> 	If you know Python programming, it wouldn't be too hard to change the
> Chimera distance-montoring code so that distance monitors change colors
> depending on whether the corresponding constraint is satisfied/violated,
> if that would help.  That code is in <chimera
> installation>/share/StructMeasure/DistMonitor.py, specifically the
> addDistance and updateDistance routines.
>
> --Eric
>
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>
> On Nov 18, 2013, at 11:56 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi George,
>> Sorry, there is nothing like that.  You would have to use some other
>> program for satisfaction of multiple constraints/restraints.
>>
>> With Chimera, it would probably be difficult depending on the number of
>> constraints, but you could measure the various distances and then move
>> one structure relative to the other; the distance values will update
>> automatically.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
>>
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> On Nov 18, 2013, at 9:16 AM, "George Patargias" <gpat at bioacademy.gr>
>> wrote:
>>
>>> Hello
>>> Do you know if there is a way to set interatomic distances to a certain
>>> value in chimera (rather than measuring them)?
>>>
>>> Basically what I want to do is rotate/translate a peptide with respect
>>> to
>>> a protein so that a set of interatomic distances between the two are
>>> satisfied
>>> Many thanks!
>>> George
>>>
>>
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>
>


Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568



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