- IMP-users - salilab.org

IMP 2.22.0 release
by Ben Webb 12 Dec '24

12 Dec '24

IMP 2.22.0 is now available. This adds the Bayesian Fluorescence Framework and improves mmCIF support. As of this release, IMP only supports Python 3; please port any Python 2 workflows to Python 3. See https://integrativemodeling.org/2.22.0/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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Requesting assistance: certain information on your website is not loading properly
by Isabella Parker 21 Oct '24

21 Oct '24

Hi! I'm having difficulty loading some pages on your website, integrativemodeling.org. Could you let me know who I should contact to resolve this issue? Thank you for your help! Best regards!

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IMP 2.21.0 release
by Ben Webb 13 Jun '24

13 Jun '24

IMP 2.21.0 is now available. This adds support for spatiotemporal modeling and nested sampling-based optimization of representation. This is also the last version of IMP to support Python 2; please port your workflows to Python 3. See https://integrativemodeling.org/2.21.0/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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IMP 2.20.2 release
by Ben Webb 04 Apr '24

04 Apr '24

IMP 2.20.2 is now available. This is a minor bugfix release, correcting build issues with Boost 1.84 and latest SWIG, and adding support for ARM64 .deb packages. See https://integrativemodeling.org/2.20.2/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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Python 2 deprecation in IMP
by Ben Webb 01 Mar '24

01 Mar '24

Hello everyone - I just wanted to give plenty of notice that we will be dropping support for Python 2 in IMP in a few months. As you are undoubtedly aware, Python 2 was officially retired several years ago, and it is becoming increasingly difficult to support it. Thus, when RedHat Enterprise 7 (which still ships with Python 2) reaches end-of-maintenance on June 30th 2024, we will drop Python 2 support in the next stable IMP release. Likely at this time we will also drop the legacy Mac .dmg installer, which only supports the older x86_64 Macs anyway (we recommend using conda or Homebrew to get IMP on a Mac). If this would cause a lot of issues with your own workflows and for some reason you cannot move to Python 3, please let me know or update the relevant GitHub issue: https://github.com/salilab/imp/issues/1092 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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IMP 2.20.1 release
by Ben Webb 16 Jan '24

16 Jan '24

IMP 2.20.1 is now available. This is a minor bugfix release, introducing compatibility with Python 3.12 and SWIG 4.2, and fixing a crash in the soap_score tool when scoring multiple models with an orientation-dependent SOAP score. See https://integrativemodeling.org/2.20.1/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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crosslinkingMS database with custom ambiguity groups
by Andrea Graziadei 02 Jan '24

02 Jan '24

Hello, I have a crosslinking MS dataset beteween 3 proteins, A, B and C. B and C are different proteins that share 30% identical sequence in chunks. Thus, I have crosslinks from A to B that are unambiguous, and others that may be from A to B or from A to C, as they go to a shared sequence. For homodimers, IMP handles this automatically. How do I construct the crosslink database to specify ambiguity at the restraint level? is there a column I can add to the crosslink csv that has a a selection e.g. residue 5 of protein A is crosslinked to residue 17 of protein B or residue 29 of protein C? Many thanks, Andrea

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IMP 2.20.0 release
by Ben Webb 21 Dec '23

21 Dec '23

IMP 2.20.0 is now available. This includes improved support for mmCIF files, reduced memory utilization, and preliminary support for converting RMF format directly to mmCIF. See https://integrativemodeling.org/2.20.0/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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IMP usage question
by yann.sterckx＠uantwerpen.be 12 Dec '23

12 Dec '23

Hi, I'm very new to IMP and have perhaps a naive question. We are working on a protein that is partially intrinsically disordered. We have a conformational ensemble that nicely fits to SAXS data set, but our aim is to include data from other methods to refine the ensemble. We have CD spectroscopy data and CCS from ion mobility MS. We were wondering whether IMP is suited to calculate the conformational ensemble using all three data sources (SAXS, CD spectroscopy, CCS by ion mobility MS) as input restraints? Clearly, IMP can handle the SAXS, but handling of CD and CCS was less clear to us. Thank you and best wishes, Yann

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IMP 2.19.0 release
by Ben Webb 23 Jun '23

23 Jun '23

IMP 2.19.0 is now available. This contains serialization support for many commonly-used IMP classes, and support for capturing information on most IMP restraints in output RMF files. See https://integrativemodeling.org/2.19.0/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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