On 3/8/22 5:05 AM, Altair Hernández wrote:
> 1. Is there a way to include the MRC file for the membrane visualization
> in the final RMF? How do you do it in IMP?

No - although you can add basic geometry to RMF files if you want
(cylinders, spheres, lines). See, e.g. RMF.SegmentFactory at
https://integrativemodeling.org/rmf/motion_8py-example.html

> 2. How is the ExternalBarrier restraint conditioning the sampling?
> Should I use it to model proteins that bind to the membrane? Actually, I
> would like to sample a setup of membrane + vesicle (sphere of 50 nm of
> radius) + proteins that bind both the vesicle and the membrane (only
> bind above). Which would be the best approach for this system?

ExternalBarrier just restrains particles to stay within a sphere. It's
usually used as a convenience to stop the system as a whole from
drifting too far from the origin, so that the coordinates are more
manageable.

        Ben
--
ben@salilab.org                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
        - Sir Arthur Conan Doyle