Re: [phenixbb] real_space_refine questions

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. Regards, Daniel

On 2017-06-13, at 21:36, Pavel Afonine 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?

Thanks, Pavel