IMP-users

imp-users@salilab.org

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273 discussions

a capped dialanine in IMP
by Barak Raveh 09 Nov '22

09 Nov '22

HI, Does anyone know how I could model an alanine dipeptide in IMP? My problem is capping, I am not a big expert on dialanine but it seems common to cap the N- and C- terminals using ACE for the N-terminal and CT3 patch on the C-terminal (removing the OXT). Is that possible in IMP? Best, Barak

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Precision for integrative models
by Shruthi Viswanath 03 Jul '22

03 Jul '22

Hello IMP users, We recently developed PrISM, <https://urldefense.com/v3/__https://doi.org/10.1093/bioinformatics/btac400_… > a simple tool to annotate regions of high and low precision in integrative models. It is implemented as part of the IMP analysis pipeline (sampcon) and detailed usage is at github https://urldefense.com/v3/__https://github.com/isblab/prism__;!!LQC6Cpwp!tQ… . We hope it is useful for your systems. Happy to hear any feedback on the method. Best Shruthi

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IMP 2.17.0 release
by Ben Webb 24 Jun '22

24 Jun '22

IMP 2.17.0 is now available. This contains minor updates, with a number of performance improvements and support for newer C++ standards. See https://integrativemodeling.org/2.17.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ 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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Create topology from mmCIF
by Altair Hernández 03 May '22

03 May '22

Hi all, Is there any way to use mmCIF files with the TopologyReader in IMP.pmi? We are dealing with big files that cannot be held in PDB. Thanks a lot! Altair

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MC temperature
by Altair Hernández 30 Apr '22

30 Apr '22

Hi all, I would like to know how IMP deals with MC & Replica Exchange temperatures. In the doc it appears normalized (1.0, 2.5, 5.0). Is there a way to know its value in Kelvin? Thanks! Altair

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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 08 Mar '22

08 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 05 Mar '22

05 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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IMP 2.16.0 release
by Ben Webb 20 Dec '21

20 Dec '21

IMP 2.16.0 is now available. This contains major updates, notably improved NumPy integration, support for Python 3.10, and a faster scoring function for Monte Carlo sampling. See https://integrativemodeling.org/2.16.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ 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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