[phenixbb] positional restraints in real_space_refine?

[Tristan Croll]

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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