Re: [IMP-users] Membrane Restraint

[Ben Webb <>]

On 3/7/22 7:56 AM, Altair Hernández wrote:
> I would like to use IMP to restrict some proteins to be close to a 
> membrane (but not in the membrane).

Usually we do this by defining the membrane as a fixed object and 
restraining the particles relative to it. For example the membrane 
restraint you found assumes an infinite membrane in the xy plane, and 
simply restrains particles by their z coordinates. Another example would 
be a pore where the membrane is represented by a torus and particles are 
restrained based on their distance to its surface. See the IMP.npc 
module for those restraints (although those are for PMI1; they would 
need some minor modifications to work with modern PMI).

> I was checking out the 
> IMP.pmi.MembraneRestraint class, but no clue about its usage.

Normally you would not use the C++ class directly, but the Python 
wrapper, in IMP.pmi.basic.restraints. That's fairly well documented:
https://integrativemodeling.org/2.16.0/doc/ref/restraints_2basic_8py_source.html

> Is there any example I can follow?

https://integrativemodeling.org/2.16.0/doc/ref/pmi_2membrane_8py-example.html

> Is IMP creating a membrane instance (displayable in RMF files) or is it 
> only a restraint instance?

It's just a restraint, although there is a method that creates an MRC 
file for visualization purposes.

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