[phenixbb] positional restraints in real_space_refine?

Tristan Croll tic20 at cam.ac.uk
Mon Oct 7 09:14:33 PDT 2019

Ok. I've been a bit tied up today, but will try to get them together 
tomorrow. If you have access to a powerful enough GPU machine and the 
changes aren't *too* large, you could try the following right now:

- Load your model/map in ChimeraX, start ISOLDE and associate the model 
with the map, ready to go
- Add hydrogens if you haven't already using the 'addh' command on the 
ChimeraX command line
- Assuming your model is #1 (check the Models panel if you're not sure), 
do 'isolde restrain distances #1' to set up a web of distance restraints
- On the ISOLDE 'Sim settings' tab, increase the mask radius to the 
approximate distance necessary to cover the biggest move you expect
- Click the 'Show map settings dialogue' button and reduce the Weight 
term to about half (generally when you're doing big moves you want the 
map to pull quite weakly)
- Start a simulation covering the whole model ('select #1', then press 
ISOLDE's play button)
- Reduce the display to a backbone trace by hiding everything but the CA 
and P atoms: 'hide ~@CA,P'
- select the atoms you want to tug on (e.g. 'select /A:20-30')
- click the 'tug selected atoms' button (third from bottom left on the 
ISOLDE panel)
- Now, clicking and dragging with the right mouse button will tug on the 
selection - line it up so the direction you want to pull is in the plane 
of the screen, and go for it. I find that tugging in short bursts rather 
than one continuous pull yields the best results. The distance 
restraints are designed to restrain local geometry while allowing large 
conformational changes, so in general things should remain under 
control. If you need to (i.e. in places where the conformation *really* 
changes) you can release the restraints on some atoms by selecting them, 
then typing the command, 'isolde release distances sel'.

Best regards,


On 2019-10-07 10:09, Daniel Larsson wrote:
> 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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