- IMP-users - salilab.org

Is the hydration layer not used outside of fitting?
by sammahdi1994＠yahoo.com 08 Feb '23

08 Feb '23

I'm attempting to generate purely a theoretical saxs profile with no fitting. I noticed in the output and in the manual, it doesn't appear that the hydration layer is taken into account in FOXS when it comes to no fitting. The only options are to set ranges, but again, these are only used for fitting. I'm looking for something similar to crysol where you can indicate the solvent density exactly even without fitting.

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How to use zip PDBs with IMP-FOXS (such as with the online version of FOXS)
by sammahdi1994＠yahoo.com 19 Jan '23

19 Jan '23

Hello, I am attempting to run FOXS with 200+ PDBs. For this purpose I have downloaded IMP since the online version of FOXS can only use 100PDBs. However, I don't see an option in the tutorial or the help command for uploading a zip containing multiple PDBs. It appears you have to upload the PDBs individually from what I can see. This is what I'm entering: >>>foxs -g -h pdb.zip saxs_data.dat begin IMP::atom::`anonymous-namespace'::read_pdb: WARNING Sorry, unable to read atoms from PDB file. Thanks for the effort. end IMP::atom::`anonymous-namespace'::read_pdb WARNING can't parse input file pdb.zip

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IMP 2.18.0 release
by Ben Webb 15 Dec '22

15 Dec '22

IMP 2.18.0 is now available. This contains minor updates, including preliminary support for serialization, improvements in constructing topology from primary sequence, and support for the PrISM method for annotation of ensemble precision. See https://integrativemodeling.org/2.18.0/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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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 02 Jul '22

02 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 23 Jun '22

23 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 29 Apr '22

29 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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