IMP-users December 2019

imp-users@salilab.org

4 participants
5 discussions

EnvelopeScore and MapDistanceTransform
by Jan Kosinski 14 Jan '20

14 Jan '20

Dear Ben, Would it be possible to expose IMP::em::EnvelopeScore and IMP::em::MapDistanceTransform in the Python layer? Best, Jan

2 4

Error in Conjugate Gradient Optimization
by Altair Hernández Chinchilla 07 Jan '20

07 Jan '20

Hi there, I am currently using IMP to generate several models in which I apply a set of 62 restraints, plus ExcludeVolume (I work with XYZR sphere decorators). When I try to run the script 1000 times in order to generate 1000 different models, it work. However, when I try to run it 50.000 times, it came up with an error: *The script does the following:* o = IMP.core.ConjugateGradients(model_to_optimize) o.set_scoring_function(scoring_function) # this method return the scoring function that is being used o.optimize(num_iterations) # The maximum number of iteration of the optimizer to perform. # Returns the final score *When I try to run it a lot of times, the following error come up:* """ Traceback (most recent call last): File "/home/altair/bin/pycharm-community-2019.2.3/helpers/pydev/pydevd.py", line 1415, in _exec pydev_imports.execfile(file, globals, locals) # execute the script File "/home/altair/bin/pycharm-community-2019.2.3/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile exec(compile(contents+"\n", file, 'exec'), glob, loc) File "/home/altair/PycharmProjects/IMP/SCRIPTS_ALTAIR/scripts/exocyst_architecture.py", line 18, in <module> * n=50000*, tags=False, log_file=False) File "/home/altair/PycharmProjects/IMP/SCRIPTS_ALTAIR/scripts/exocyst_main.py", line 655, in create_models * conjugate_gradient_optimization*(model, sf, num_iterations) # OPTIMIZATION STEP # File "/home/altair/PycharmProjects/IMP/SCRIPTS_ALTAIR/scripts/exocyst_main.py", line 223, in conjugate_gradient_optimization * o.optimize(num_iterations)* # The maximum number of iteration of the optimizer to perform. File "/home/altair/anaconda3/lib/python3.7/site-packages/IMP/__init__.py", line 5804, in optimize return _IMP_kernel.Optimizer_optimize(self, max_steps) _IMP_kernel.ModelException: Failure in ConjugateGradients Process finished with exit code 1 """ What does it mean? Is it a problem on the max_steps of the Optimizer function? Why is this error comming up in the iteration 6000 ,e.g and not in the first one? Thanks you! Sincerely, Altair

2 3

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

1 0

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/

2 1

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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IMP-users December 2019