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
Great Ben, thanks a lot!
Altair
On Wed, 9 Mar 2022 at 05:08, Ben Webb ben@salilab.org wrote:
> 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 >
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Altair Hernández -
Ben Webb