IMP-users January 2020

imp-users@salilab.org

5 participants
4 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

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localisation densities
by Andrea Graziadei 09 Jan '20

09 Jan '20

Hello, I am wondering how to extract localisation probability densities from a list of RMF files and density ranges? The "actin tutorial" code results in densities that are not in the same reference frame as the models, making it impossible to add the LPDs of the selected cluster to an ihm model, or to view them on top of the rmfs. Is there an example for this? Many thanks, Andrea

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frame 1 score inf
by Atefeh Rafiei 08 Jan '20

08 Jan '20

Hi All, I am getting the following error and wondering what it is, what can cause it and if it is possible to bypass it. --- frame 1 score inf --- writing coordinates Traceback (most recent call last): File "MT-DCX-EM-6tub.py", line 281, in <module> mc1.execute_macro() File "C:\Program Files\IMP-2.10.1\python\IMP\pmi\macros.py", line 545, in execute_macro output.write_pdb_best_scoring(score) File "C:\Program Files\IMP-2.10.1\python\IMP\pmi\output.py", line 367, in write_pdb_best_scoring exec(open(self.best_score_file_name).read()) File "<string>", line 1, in <module> NameError: name 'inf' is not defined It is for modeling of a protein system that was working well when using only crosslinking data, but giving me this error when trying to use either EM or EM + XL as scoring functions. The same EM map and configuration is working fine for a very similar domain (same fold, very similar size). So not sure why it wouldn't work in this case. Regards, Atefeh

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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

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IMP-users January 2020