[phenixbb] positional restraints in real_space_refine?

[Daniel Larsson]

Tristan, it would be very nice if you could write it up. Thank you so much!

Regards,
Daniel



> On 2019-10-04, at 23:09, Tristan Croll <tic20 at cam.ac.uk> wrote:
> 
> I’ve done something quite like this in ISOLDE with a fair bit of success: rigid-body docked individual domains into density, then using these to define target positions for flexible fitting of the unbroken complete model from a markedly different configuration. This currently requires a little work in the ChimeraX shell to set up, but is fairly straightforward. Let me know if you’re interested and I can write up some instructions.
> 
> 
> 
> Tristan Croll
> Research Fellow
> Cambridge Institute for Medical Research
> University of Cambridge CB2 0XY
> 
> 
> 
> 
>> On 3 Oct 2019, at 11:24, Daniel Larsson <daniel.larsson at icm.uu.se> wrote:
>> 
>> Hi all,
>> 
>> I'm working on a cryo-EM reconstruction where I have some flexible low-resolution elements (RNA double helices). They have different orientations relative to my reference model, but I would like to model them in the approximately correct position. I've tried real_space_refine with morphing and simulated annealing, but neither accomplish what I want. Now I'm thinking of cutting out these helices and manually position them approximately where I want them. But I fear that this will case headache at the "joint". Is it possible to use the manual positions as a reference for positional restraints, but use the original model as the reference for the torsion angles. Is this possible with real_space_refine? Or is there a better way of refining this structure?
>> 
>> Regards,
>> Daniel
>> 
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>> 
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