September 2016 - IMP-users

accuracy and get_average_distance_wrt_reference_structure()
by Julian 13 Oct '16

13 Oct '16

Dear IMP, While playing around with the tutorial, I noticed that the accuracy calculation errors out: imp_tutorial/rnapolii/analysis/accuracy.py Traceback (most recent call last): File "accuracy.py", line 43, in <module> pr.set_reference_structure(reference_rmf,0) File "/home/jmintser/IMP/imp-2.6.2_release/lib/IMP/pmi/analysis.py", line 898, in set_reference_structure particles_resolution_one = self._get_structure(rmf_frame_index,rmf_name) File "/home/jmintser/IMP/imp-2.6.2_release/lib/IMP/pmi/analysis.py", line 524, in _get_structure IMP.rmf.link_hierarchies(rh, self.prots) File "/home/jmintser/IMP/imp-2.6.2_release/lib/IMP/rmf/__init__.py", line 501, in link_hierarchies return _IMP_rmf.link_hierarchies(*args) _IMP_kernel.ValueException: Number of children doesn't match the number of representation nodes at Rpb1. They are 4 and 3 respectively. [2, 8, 1432, 1585] vs [Beads(representation, n3), Rpb1_Res:1(representation, n9), Rpb1_Res:10(representation, n1433)] WARNING No frames were loaded from file "HierarchyLoadLink52" even though objects were linked or created. As far as I understand this is because the representation details in the native.rmf3 do not exactly match those of the modeled system. This got me thinking about how the native.rmf3 was generated in the first place. The only way I can think of making a native rmf3 is to essentially run the modeling script keeping everything rigid and not shuffling the initial configuration. Is there no way to compare the model to an existing pdb if one exists without worrying about reproducing the representation exactly? Thanks much, Julian

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crosslinking with multiple copies of subunits
by Josh Bullock 04 Oct '16

04 Oct '16

Hello IMP Users, I was wondering, how does IMP handle crosslinks when there are multiple copies of the same subunit (created in IMP using the create_clone() function) ? If an inter-subunit crosslink is satisfied in IMP with an intra-crosslink, does this stop the crosslink from contributing to the scoring ? Also, experimentally it is possible to clarify which crosslinks are definitely intra-subunit (via SDS-PAGE). However there doesn't seem to be any way to flag this on a crosslink in IMP, unless I'm missing something ... ? Thanks, Josh

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ideal_helix as part of multiscale model
by Julian 05 Sep '16

05 Sep '16

Dear IMP, I recently started playing around with IMP and was thinking that it would be great to be able to specify secondary structures, especially helices instead of beads. So for example if I have a homology model for a domain or two and want to model the full length protein, I would specify the rest of sequence as beads of some size in the topology file. However if I had a reasonably confident prediction of helices, I could specify what would be essentially "rods" instead of "beads". It seems to me that might help get the geometry right in some situations. I do see that there's a way to add_representation(mol, resolutions=[1,10], ideal_helix=True) but don't quite see how I can wedge that into a multiscale topology of a model. Thanks much, Julian

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ReplicaExchange: Could not find MPI. Using Serial Replica Exchange
by Julian 01 Sep '16

01 Sep '16

Hi, I'm trying to run the exosome example with MPI but can't seem to get it to work. I installed binaries both on Fedora 19 and Ubuntu Trusty. I have openmpi on both and mpich on Fedora as well. mpirun is in my path. Do I need to build with MPI mysefl for this to work or is this supposed to work with binaries out of the box? Thanks, Julian

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