IMP-users

imp-users@salilab.org

273 discussions

Modeling the relation between two complexes with a common protein and linking region between
by Gorbea, Jose 28 May '20

28 May '20

Hi all, I hope you are doing well. I am trying to model the position of a small protein complex within a larger assembly based on EM, crosslinking data, and high-resolution structures of the individual complexes in PDB format, but I am having a bit of an issue getting things to work properly. Specifically, the small complex is made up of three proteins with one of these physically linking the two complexes together. Two regions in the linking protein are highly resolved within each complex, with a flexible linker in between. As such, I would simply like to simulate the two complexes as rigid bodies, have the linking region be flexible, and observe how the small complex may fill a low-resolution volume within the EM, as informed by XL-MS data and the linking protein region. However, when I attempt the simulation, the fragment of the linker protein supposed to attach to the larger complex is not static relative to the larger complex. I think this may be either an issue with system representation in the topology file or perhaps something else that the community may have faced before and could help me out with. I would appreciate any suggestions you may have. Best, Jose

1 0

IMP 2.13.0 release
by Ben Webb 14 May '20

14 May '20

IMP 2.13.0 is now available. This is contains major updates, most notably support for Ubuntu 20.04, Focal Fossa, and a new IMP::sampcon module to estimate the highest precision at which the sampling is exhaustive. See https://integrativemodeling.org/2.13.0/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

IMP DiameterRestraint
by Altair Hernández 16 Apr '20

16 Apr '20

Hi IMP users, I used to work with a Diameter restraint in the past using IMP version 2.2 where I specified in a XML file the *max_diameter* and *std_dev* between pairs of particles. I would like to know how to use this function with the latest version of IMP (2.12). Also I would be grateful to know which is the main difference between the DiameterRestraint and the Harmonic Upper Bound, and how to justify a given k value when using the HarmonicUpperBound restraint. Thank you! Altair

2 2

Error when sampling antibody conformations using rrt_sample
by Fisher H. 08 Apr '20

08 Apr '20

Hi, I was just wondering if I could get some information on an error I’m getting when trying to run antibody conformational sampling using the rrt_sample. ERROR: IMP currently does not support switching of parents in a kinematic tree What does this mean and is there a way to fix it? Thanks, Hayden Hayden Fisher | PhD Student Structural Biology, Integrative Modelling and Cancer Sciences University of Southampton

2 1

restarting a run
by Andrea Graziadei 09 Mar '20

09 Mar '20

Hello IMPers, I was wondering if there is a way to restart a PMI ReplicaExchange0 run that crashed half way through or extend a run that has finished from a set of rmf and stat files. Is this possible? Many thanks, Andrea

2 1

Custom Hierarchy
by Altair Hernández Chinchilla 10 Feb '20

10 Feb '20

Hi IMP users, I am currently working with no PDB structure, but with a custom artifact proteins made of concatenated beads (IMP spheres with volume). I would like to apply and integrate different type of data on it (cross linking - mass spectrometry, yeast two-hybrid, and cryoEM). I would like to ask you if should I work with hierarchies (IMP.atom.Hierarchy <https://integrativemodeling.org/2.12.0/doc/ref/classIMP_1_1atom_1_1Hierarch…>or IMP.core.Hierarchy) in this case, customizing my hole complex of 8 subunits with different molecules and atoms. If it is the case, how can I work on it in the way that I can parse the full molecule like: """ for molecule in root.get_children(): for atom in molecule.get_children(): do sth """ I have been trying on it, but no way to track the full hierarchy. I would appreciate some help, or just an example to how work on it. Or may be there is no sense to. For instance, the IMP.core.ConnectivityRestraint example <https://integrativemodeling.org/2.12.0/doc/ref/classIMP_1_1core_1_1Connecti…> makes hierarchies but is not parsing the full molecule, only connecting all the beads. I would like to force it to only a pair of fragments to be connected in a certain distance. Some advice for it? Should I work on it if needing to integrate cryoEM data with IMP.pmi? Thanks in advance! Altair

3 4

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

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

2 1

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

2 1

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

← Newer
1
2
3
4
5
6
7
8
9
...
28
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

IMP-users