March 2022 - IMP-users

Returning original atom coordinates after sampling
by Altair Hernández 29 Mar '22

29 Mar '22

Hi there, Is there any way that IMP returns the original atomic coordinates after sampling? Thanks! Altair

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Re: [IMP-users] Membrane Restraint
by Ben Webb 10 Mar '22

10 Mar '22

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(a)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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Membrane Restraint
by Altair Hernández 07 Mar '22

07 Mar '22

Hi, I would like to use IMP to restrict some proteins to be close to a membrane (but not in the membrane). I was checking out the IMP.pmi.MembraneRestraint class, but no clue about its usage. Is there any example I can follow? Is IMP creating a membrane instance (displayable in RMF files) or is it only a restraint instance? Thanks! Altair

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DNA modeling
by Altair Hernández 04 Mar '22

04 Mar '22

Hi all, I am trying to model a system with DNA and TF (transcription factors) that bind both the DNA and other TFs. When using IMP.pmi, I find that the output PDB models for the DNA replace the base pairs by Alanines (ALA) for one of the DNA strands. Instead, for the other strand it keeps it as original. Why could this be happening? Thanks! Altair

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