[phenixbb] real_space_refine questions
daniel.larsson at icm.uu.se
Wed Jun 14 00:25:57 PDT 2017
Thanks for the suggestions Oleg. I will prepare input files for you Pavel.
I also noticed that if I want to apply NCS between some chains, the model gets very distorted. The initial chains are very similar, but during the first macro cycle the selection molecules "jump" into a funny position, totally different from the initial position. It is as if the initial optimization of the NCS operator fails. I'll bundle a run script that reproduces that effect at the same time.
> On 2017-06-13, at 21:36, Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Daniel,
>> - Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops?
> as Oleg pointed out reference model restraints (to restrain to initial position) should do the trick.
>> - When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm?
> Technically this can happen but so far I've never seen this actually happening. Would it be possible to send me map and model files so that I can reproduce what you describe and attempt to find a solution?
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