November 2017 - IMP-users

Floppy bodies
by Komjati Kornel 30 Nov '17

30 Nov '17

Hi all, My name is Kornel and I am trying to define a protein as a chain of rigid and floppy bodies. With the help of the online manual I worked out how to define rigid bodies, but for floppy bodies I have not found a solution. My sample topology looks like this: |component_name|domain_name|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian| |CHAIN_A| RIGID_1 |fasta.txt| ID:A |protein.pdb |A| 121,150| 0| 30|0| |CHAIN_A| FLOPPY_1 |fasta.txt| ID:A |protein.pdb |A| 151,180| 0| 5|0| |CHAIN_A| RIGID_2 |fasta.txt| ID:A |protein.pdb |A| 181,220| 0| 30|0| |CHAIN_A| FLOPPY_2 |fasta.txt| ID:A |protein.pdb |A| 221,280| 0| 5|0| And the modeling.py looks like this: m = IMP.Model() topology = IMP.pmi.topology.TopologyReader(topology_file) domains = topology.get_components() rigid_bodies = [["RIGID_1"],["RIGID_2"]] bm = IMP.pmi.macros.BuildModel(m, component_topologies=domains, list_of_rigid_bodies=rigid_bodies) So my question is: what is the correct way to define domains as floppy bodies? Thanks, Kornel

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run clustering.py on multiple stat files
by מירב בריטברד 30 Nov '17

30 Nov '17

Hi, I ran modeling.py multiple times and created different output folders that each of them contain a stat file. Now I want to run clustering.py on all the stat files in the different folders, how can I do it? Thank, Merav

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IMP bug - decorating floppy bodies as gaussians
by Fergal Duffy 21 Nov '17

21 Nov '17

I seem to have run into a bug while trying to use a cryoEM restraint with IMP.pmi 2.8.0. Reading the BuildSystem code, it looks like it will add individual gaussians to the flexible beads as long as a non-zero value is given for the em_residues_per_gaussian column in the topology file. However, this then crashes when the system is shuffled with IMP.pmi.tools.shuffle_configuration. If I do not shuffle the system and start the simulation via the IMP.pmi.macros.ReplicaExchange0 routine, I get the same error while performing replica exchange. I am setting up my complex using a topology file and the BuildSystem macro, following the code below. m = IMP.Model() topology = IMP.pmi.topology.TopologyReader(topology_file, pdb_dir=os.path.join("data/PDBs"), fasta_dir=os.path.join("data/Sequences"), gmm_dir=os.path.join("data/subunitEMs")) bs = IMP.pmi.macros.BuildSystem(m, resolutions=[1,10]) bs.add_state(topology) root_hier, dof = bs.execute_macro() #Add restraints.. <snip> # IMP.pmi.tools.shuffle_configuration(root_hier) This fails with the following error: shuffling 23 rigid bodies shuffling 186 flexible beads Traceback (most recent call last): File "..\modelling\simulate_tfiid.py", line 690, in <module> main() File "..\modelling\simulate_tfiid.py", line 686, in main simulation = TFIIDModelling(parser.parse_args()) File "..\modelling\simulate_tfiid.py", line 333, in __init__ self.initialise() File "..\modelling\simulate_tfiid.py", line 357, in initialise tools.shuffle_configuration(self.root_hier) File "C:\Users\fduffy\AppData\Local\Continuum\Anaconda2\envs\IMP\lib\site-packages\IMP\pmi\tools.py", line 2087, in shuffle_configuration IMP.core.transform(d, transformation) File "C:\Users\fduffy\AppData\Local\Continuum\Anaconda2\envs\IMP\lib\site-packages\IMP\core\__init__.py", line 8878, in transform return _IMP_core.transform(*args) _IMP_kernel.UsageException: Usage check failure: Particle is also a RigidBody, so this function would do the wrong thing; decorate your Particle as a RigidBody instead and call transform(RigidBody a, const algebra::Transformation3D &tr) Looking at the tools.shuffle_configuration code, the problem seems to lie around line 2111, where <https://github.com/salilab/imp/blob/develop/modules/pmi/pyext/src/tools.py> 1987 rigid_bodies,flexible_beads = get_rbs_and_beads(hierarchies) ... 2090 for fb in flexible_beads: ... 2110 # For gaussians, treat this fb as an rb 2111 if IMP.core.NonRigidMember.get_is_setup(fb): 2112 xyz=[fb.get_value(IMP.FloatKey(4)), fb.get_value(IMP.FloatKey(5)), fb.get_value(IMP.FloatKey(6))] ... 2126 else: 2127 d =IMP.core.XYZ(fb) Presumably, the IMP.core.NonRigidMember.get_is_setup(fb) call should return True for floppy bodies with gaussians, but it currently is returning False, which causes the co-ordinate transformation to fail. Is there any easy solution or workaround for this? Fergal Duffy Staff Scientist Center for Infectious Disease Research<http://www.cidresearch.org/> 307 Westlake Ave N, Suite 500 | Seattle, WA 98109 206.256.7435 | fergal.duffy(a)cidresearch.org<mailto:fergal.duffy@cidresearch.org>

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Re: [IMP-users] MPI setup
by Ben Webb 06 Nov '17

06 Nov '17

On 11/5/17 7:13 AM, מירב בריטברד wrote: > I managed to build with MPI but got a runtime error (below) This sounds like the usual OpenMPI problem documented in the IMP manual (with workarounds): https://integrativemodeling.org/2.8.0/doc/ref/namespaceIMP_1_1mpi.html > is it critical to run replica exchange in order to get the best results > or Monte Carlo is also ok? If you don't have MPI you'll just get replica exchange with one replica, which will give you less complete sampling, of course. 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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MPI setup
by מירב בריטברד 02 Nov '17

02 Nov '17

Hi, I have a problem configuring MPI, I get the message bellow. How can I get more details about what is missing? thanks, Merav -- MPI found mpi is disabled Module IMP.mpi disabled

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