Re: [IMP-users] Problem with IMP.core.TransformationSymmetry

[Jan Kosinski <>]

Hi Ben,

So, the solution you proposed is to use IMP.atom.create_compatible_rigid_body() for all but the first rigid body. That is fine and indeed works for the example script. Thanks a lot!

But if one uses the nice DegreesOfFreedom class to create rigid bodies via DegreesOfFreedom.create_rigid_body function, it won’t be possible to use this fix - the DegreesOfFreedom.create_rigid_body function uses IMP.atom.create_rigid_body and does not allow to optionally use IMP.atom.create_compatible_rigid_body.

And, actually why the reference frames of the same structure read twice cannot be guaranteed to be the same?

Best,
Jan

> On 20. Nov 2020, at 19:32, Ben Webb <> wrote:
> 
> What problem are you trying to solve here?
> 
> 	Ben
> 
> On 11/19/20 11:34 AM, Jan Kosinski wrote:
>> Thanks, will test it! Do you think it could be added as an option also to DegreesOfFreedom.create_rigid_body ?
>> Best,
>> Jan
>>> On 19. Nov 2020, at 01:20, Ben Webb <> wrote:
>>> 
>>> Tracked and resolved at https://github.com/salilab/imp/issues/1032
>>> 
>>> 
>>> On 8/26/20 11:09 AM, Ben Webb wrote:
>>>> On 8/25/20 5:47 AM, Jan Kosinski wrote:
>>>>> OKay, I see, I think it’s like you suggest, but I have to add some crazy code block to update the members, as below in bold:
>>>> ...
>>>>> *#crazy code block:*
>>>>> *for rb in rbs:*
>>>>> *    rb.update_members()*
>>>>> *m.update()*
>>>>> *for rb in rbs:*
>>>>> *    rb.set_reference_frame(rb.get_reference_frame()) #this updates the members immediately too*
>>>>> *m.update()*
>>>>> *#end of the crazy code block*
>>>> Hmm, this sounds like something isn't right with the dependencies, so updates aren't happening automatically in the right order (although odd that it works for some chains and not others). I'll open an issue.
>>>>     Ben
>>> 
>>> 
>>> -- 
>>>                       https://salilab.org/~ben/
>>> "It is a capital mistake to theorize before one has data."
>>> 	- Sir Arthur Conan Doyle
> 
> 
> -- 
>                       https://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> 	- Sir Arthur Conan Doyle
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