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imp-users@salilab.org

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273 discussions

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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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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