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273 discussions

IMP 2.12.0 release
by Ben Webb 06 Dec '19

06 Dec '19

IMP 2.12.0 is now available. This is contains major updates, most notably support for Python 3.8 and RHEL/CentOS 8, and a new IMP::bayesianem module for Bayesian handling of cryo-electron microscopy density map data. See https://integrativemodeling.org/2.12.0/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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mmcif creation with DNA
by Lenz, Swantje 05 Dec '19

05 Dec '19

Hello, I am building a system using PMI and IMP.pmi.topology.TopologyReader. I have proteins, DNA and RNA. In my PDBs, the DNA is encoded as DA, DC,DT,DG and the RNA as A,C,U,G. In topology, I specify the objects as DNA and RNA: |DNA1N |dark magenta|myfasta.fasta|DNAN,DNA |longRNAR1 |magenta |myfasta.fasta|longRNAR,RNA| If I have A,C,G,U and T in my fasta file I get the following warnings and errors for DNA.WARNING: Inconsistency between FASTA sequence and PDB sequence. FASTA type 1 "G" and PDB type "DG" WARNING: Inconsistency between FASTA sequence and PDB sequence. FASTA type 2 "G" and PDB type "DG" WARNING: Inconsistency between FASTA sequence and PDB sequence. FASTA type 3 "G" and PDB type "DG"The script then continues and modeling proceeds. However, when I try to implement the "deposition" part covered in https://integrativemodeling.org/tutorials/deposition/ , there are several errors due to not recognizing residue types, since the alphabet is defined as the peptide alphabet in the ihm module by default. How should the DNA be encoded in the fasta file? Additionally, we have two copies of one protein. This causes the second copy to not be created as an asymmetric unit in create_component in the protocol output of mmcif.py. We could fix this by changing the function as followed: def create_component(self, state, name, modeled, asym_name=None): if asym_name is None: asym_name = name new_comp = name not in self._all_components self._all_components[name] = None if modeled: state.all_modeled_components.append(name) self.asym_units[asym_name] = None # this was originally in the if statement below if new_comp: # assign asym once we get sequence self.all_modeled_components.append(name)? Thanks, Swantje ? -- ________________________________ Swantje Lenz M. Sc. Biotechnology Fachgebiet Bioanalytik (TIB 4/4-3), Institut für Biotechnologie, Technische Universität Berlin Technische Universität Berlin | Gustav-Meyer-Allee 25 | Gebäude 17a | 13355 Berlin Tel +49 30 314-72906 | web: http://www.bioanalytik.tu-berlin.de/

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Maximum distance restraint between spheres
by Altair Hernández Chinchilla 04 Dec '19

04 Dec '19

Hi IMP users, I want to create pairwise distance restraints between IMP particles (spheres XYZR of a given radius) with a maximum distance condition.So I want a given sphere to be in a range between 0 and max distance of 17 Aº. How can I do it in IMP? Given a set of sphere pairs, and a distance between them, how can I apply a IMP function to force a maximum distance restraint in a similar way then a Harmonic function? f = IMP.core.Harmonic(float(tag_list[1]), float(tag_list[2])) s = IMP.core.DistancePairScore(f) r = IMP.core.PairRestraint(model, s, (bait_p, tag_p)) How can I substiute the IMP.core.Harmonic with a maximum distance function? Thanks in advance! Altair

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Ambiguous restraints
by Francesco RAIMONDI 05 Nov '19

05 Nov '19

Dear all, I have a set of MS/XL restraints which I'd like to use to predict the structure of a putative homodimeric protein. Some of the XL are expected to happen within the same chain, others between the two distinct chains of the homodimer. The way I tackled the ambiguity issue so far is to explicitly generate all the possible XL/chain combinations and use this expanded list as an input for an adapted version of the human complement modeling script ( https://salilab.org/Complement) using IMP v2.9. Is there a better way to deal with ambiguity in IMP? I also found the AmbiguousCompositeRestraint <https://integrativemodeling.org/2.6.1/doc/ref/classIMP_1_1pmi_1_1restraints…> class, but didn't yet manage to find an example script using it. I'd be grateful for any suggestions you could provide me in this respect. Thanks so much and all the best, Francesco

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Compiling a module out of tree
by Patrick Goetz 04 Nov '19

04 Nov '19

I'm trying to incorporate an out of tree IMP module called bayesianem. What I thought should be possible is to install the IMP Ubuntu 18.04 binary package, build bayesianem from source, and add it, but am running in to some problems. According to the IMP documentation (https://integrativemodeling.org/2.11.1/doc/manual/uselibrary.html), "When IMP is built or installed, it creates a CMake file called IMPConfig.cmake which contains information about how IMP was configured and where all the parts of IMP can be found." Unfortunately I could not find such a file anywhere on the system, but the bayesianem cmake script is clearly looking for it. Excerpted from bayesianem's source dir CMakeLists.txt: find_package(IMP REQUIRED) include(${IMP_USE_FILE}) and if I try and do the build I get: -------------------------------- By not providing "FindIMP.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "IMP", but CMake did not find one. Could not find a package configuration file provided by "IMP" with any of the following names: IMPConfig.cmake imp-config.cmake -------------------------------- I also cloned the IMP git repo, but couldn't find anything there, either. The "Building modules out of tree" page (https://integrativemodeling.org/2.11.1/doc/manual/outoftree.html) talks about a FindIMP.cmake file, but I couldn't find this anywhere either. Presumably I am doing something wrong. Can someone give me some pointers? The bayesianem git repo (https://gitlab.pasteur.fr/rpellari/bayesianem) is pretty sparse on documentation. Thanks.

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Compiling an IMP module out of tree
by Goetz, Patrick G 30 Oct '19

30 Oct '19

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BuildModel 2 BuildSystem
by Marcell Miski 26 Sep '19

26 Sep '19

Dear Imp-Users, I am trying to model a complex using IMP however, I can't use the older IMP on a server. My problem is that when I try to change to using BuildSystem, my simulation fails. I attach, the original modeling.py and the new modeling.py with the two inputs. Can you help me how to fix this? Best regards, Marcell Miski Ph.D. Student PPCU FIT BP HU

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changing the python version in IMP
by Merav Braitbard 05 Sep '19

05 Sep '19

Hi, my default version of python is 2.7, but when I tried to run imp with this version I've got an error that numpy version is old. So I tried to use python 3.7 like this: setup_environment.sh python3.7 modeling.py and I got this error: *Traceback (most recent call last): File "modeling.py", line 21, in <module> import IMP.pmi.restraints.crosslinking File "/vol/sci/bio/bio3d/meravb/Programs/imp_build_cluster/lib/IMP/__init__.py", line 11, in <module> import _IMP_kernelImportError: /vol/sci/bio/bio3d/meravb/Programs/imp_build_cluster/lib/_IMP_kernel.so: wrong ELF class: ELFCLASS64* what can I do in order to run IMP properly. Furthermore recently it takes very long time (hours) to build the IMP. Do you know why this has happened? Thanks, Merav

2 1

CrossLinkTable
by Julian 28 Aug '19

28 Aug '19

Dear IMP gurus, I'd like to get some frequency statistics for my cross-link based final model. Rather than starting from scratch, I saw tools doing more or less what I want - it seems like IMP.pmi.analysis.CrossLinkTable class methods like write_cross_link_database and get_frequency_statistics functions would be useful. A ContactMap plot would be nice but less important. To work with this class, it appears I need a single stat file, but what I have is a cluster of rmf files with a single frame each, originating from a bunch of stat files from different runs. Is there a simple way to generate a stat file from the rmfs to initialize a CrossLinkTable? Or am I going about this the wrong way? Thanks much, Julian

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IMP 2.11.1 release
by Ben Webb 18 Jul '19

18 Jul '19

IMP 2.11.1 is now available. This is a bugfix release, which fixes some issues with the build system, failures to read RMF files, and cloning of molecular hierarchies. See https://integrativemodeling.org/2.11.1/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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