- IMP-users - salilab.org

Rigid body from multiple chains
by Komjati Kornel 26 Feb '18

26 Feb '18

Hi, I would like to model a protein with multiple chains (A,B,C,D) as an entire rigid body. Unfortunately I cannot find a way to do this, it seems like that a rigid body can only contain one protein chain. Is there any method to create my desired model? Thanks in advance, Kornel

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running imp with DNA sequence
by מירב בריטברד 05 Feb '18

05 Feb '18

Hi, Part of the structure that I am trying to find is a DNA sequence and not a protein. I have pdb with the DNA part, and I create a fasta file (both attached) but when I am running IMP, it's write this warning: "BuildSystem.add_state: -------- domain 0 of molecule DNA_1 represented by pdb file /cs/labs/dina/meravb/CENP_new_cross_links_and_PDB_renumbered/pdb_files/Nuc_numbering_fixed_in_map.pdb WARNING: Replacing sequence residue 1 "THR" with PDB type "DC" WARNING: Replacing sequence residue 2 "GLY" with PDB type "DT" WARNING: Replacing sequence residue 3 "CYS" with PDB type "DG" WARNING: Replacing sequence residue 4 "ALA" with PDB type "DC" WARNING: Replacing sequence residue 5 "GLY" with PDB type "DA" WARNING: Replacing sequence residue 6 "ALA" with PDB type "DG" WARNING: Replacing sequence residue 7 "THR" with PDB type "DA" WARNING: Replacing sequence residue 8 "THR" with PDB type "DT" WARNING: Replacing sequence residue 9 "CYS" with PDB type "DT"....." How can I run in imp in a way that will recognize the DNA? Thanks, Merav

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IMP: moving a gaussian decorated flexible bead
by Fergal Duffy 30 Jan '18

30 Jan '18

Hi, I have noticed an odd thing when trying to shuffle flexible beads decorated with Gaussian particles. The code in IMP.pmi.tools.shuffle_configuration uses xyz=[fb.get_value(IMP.FloatKey(4)), fb.get_value(IMP.FloatKey(5)), fb.get_value(IMP.FloatKey(6))] to get the initial XYZ location of the Gaussian fb. However, this location does not return the same value as IMP.core.XYZ(fb) And it looks like IMP.core.XYZ is actually the correct location of the floppy body, leading to some odd results when shuffling based on the fb.get_value() based locations. What is the correct way to find the location of, and move, a Gaussian decorated flexible bead? 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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a problem with the updated IMP
by מירב בריטברד 16 Jan '18

16 Jan '18

I install an updated IMP on my computer and try to run the modeling.py script. But when I try to open the rmf file from this run in chimera I got this message: [image: Inline image 2] What can I do in order to open the rmf file and work as usual? Thanks, Merav

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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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rigid bodies and super rigid bodies
by מירב בריטברד 26 Oct '17

26 Oct '17

Hi, My name is Merav and I am working with the modeling with EM and cross links. I started from the example with rnapolii *. *I have attached my topology file. I have one PDB that contains 3 proteins and should be one rigid body (ARP7, ARP9, RT102). I also have one protein with 3 subunits that should be 3 rigid bodies (RCS2_1, RCS2_2, RCS2_3) and should belong to the super rigid body. What would be the right way to specify that in the topology file? or should it be done in the script like in rnapolii example (which is not clear either)? thanks, Merav

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