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ideal_helix density
by Julian 03 Nov '16

03 Nov '16

Dear IMP, I'm trying to figure out how one would use the IDEAL_HELIX representation for purposes of EMRestraint. I'm working with the tutorial example and the representation looks like this: m = IMP.Model() representation = IMP.pmi.representation.Representation(m,upperharmonic=True, disorderedlength=False) # compname hier_name color fastafile fastaid pdbname chain resrange read beadsize rigid_body super_rigid_body emnum_components, emtxtfilename emmrcfilename domains=[("Rpb1", "Rpb1_1", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:A", datadir+"1WCM_map_fitted.pdb", "A", (1,1140,0), True, 20, None, None, 57, None, None, None), ("Rpb1", "Rpb1_2", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:A", datadir+"1WCM_map_fitted.pdb", "A", (1141,1274,0), True, 20, None, None, 7, None, None, None), ("Rpb1", "Rpb1_3", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:A", datadir+"1WCM_map_fitted.pdb", "A", (1275,1455,0), True, 20, None, None, 9, None, None, None), ("Rpb2", "Rpb2_1", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:B", datadir+"1WCM_map_fitted.pdb", "B", (1,1102,0), True, 20, None, None, 55, None, None, None), ("Rpb2", "Rpb2_2", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:B", datadir+"1WCM_map_fitted.pdb", "B", (1103,-1,0), True, 20, None, None, 6, None, None, None), ("Rpb3", "Rpb3", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:C", datadir+"1WCM_map_fitted.pdb", "C", (1,-1,0), True, 20, None, None, 16, None, None, None), ("Rpb4", "Rpb4_1", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:D", "BEADS", None, (1,54,0), True, 20, 1, [1], 0, None, None, [1]), ("Rpb4", "Rpb4_2", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:D", "IDEAL_HELIX", None, (55,75,0), True, 1, 1, [1], 20, None, None, [1]), ("Rpb4", "Rpb4_3", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:D", "BEADS", None, (76,-1,0), True, 20, 1, [1], 0, None, None, [1]), ("Rpb5", "Rpb5", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:E", datadir+"1WCM_map_fitted.pdb", "E", (1,-1,0), True, 20, None, None, 11, None, None, None), ("Rpb6", "Rpb6", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:F", datadir+"1WCM_map_fitted.pdb", "F", (1,-1,0), True, 20, None, None, 8, None, None, None), ("Rpb7", "Rpb7", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:G", "BEADS", None, (1,-1,0), True, 20, 4, [4], 0, None, None, [4]), ("Rpb8", "Rpb8", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:H", datadir+"1WCM_map_fitted.pdb", "H", (1,-1,0), True, 20, None, None, 7, None, None, None), ("Rpb9", "Rpb9", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:I", datadir+"1WCM_map_fitted.pdb", "I", (1,-1,0), True, 20, None, None, 6, None, None, None), ("Rpb10", "Rpb10", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:J", datadir+"1WCM_map_fitted.pdb", "J", (1,-1,0), True, 20, None, None, 4, None, None, None), ("Rpb11", "Rpb11", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:K", datadir+"1WCM_map_fitted.pdb", "K", (1,-1,0), True, 20, None, None, 6, None, None, None), ("Rpb12", "Rpb12", 0.00, datadir+"1WCM_new.fasta.txt", "1WCM:L", datadir+"1WCM_map_fitted.pdb", "L", (1,-1,0), True, 20, None, None, 4, None, None, None)] bm1 = IMP.pmi.macros.BuildModel1(representation) bm1.build_model(domains) When I was modeling Rpb4 and Rpb7 as BEADS, everything seemed to be working. I then tried modeling a stretch of Rpb4 as IDEAL_HELIX, but I'm not sure the density of that helix is recognized and the representation/density doesn't look they way I would expect in Chimera. I thought I should have it represented by 1 bead/aa. I basically just want to model it as a straight tube both for representational and EM density purposes. Thanks much, Julian

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IMP.pmi.restraints.em.GaussianEMRestraint vs IMP.em.EnvelopeFitRestraint
by Julian 03 Nov '16

03 Nov '16

Hi, I was wondering what the difference is between the different EM restraints. The doc says EnvelopeFitRestraint may be faster for low-res maps but that's about it. The only place I could find using it is the pde6 exampe. I tried using it in the tutorial example instead of the GaussianEMRestraint but couldn't get it to work. I guess I don't really understand what kind of particles are expected in IMP.em.EnvelopeFitRestraint(particles, map, 11.0, 5.0) Would this restraint work with the ReplicaExchange anyway? Thanks a lot, Julain

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Upcoming joint IMP and NAMD/VMD workshop at UCSF next month
by Ben Webb 03 Nov '16

03 Nov '16

I just wanted to bring everyone's attention to a hands-on workshop that we'll be hosting next month (Dec 12-16) here at UCSF: https://www-s.ks.uiuc.edu/Training/Workshop/SanFrancisco2016/index.html This is a week long joint workshop in conjunction with the folks from TCBG at UIUC. Between us we'll be covering both IMP and TCBG tools such as NAMD and VMD. We'll have time to really look at a number of applications of IMP to biophysical systems in detail. This is a small workshop (25 attendees). Application deadline is Nov 18th. Please let me know if you have any questions about the workshop. 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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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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save values of RestraintsScoringFunction to RMF
by Jan Kosinski 24 Jun '16

24 Jun '16

Hi, Is it possible to save the total score to the RMF file with IMP.rmf.SaveOptimizerState? Basically, I am saving a Monte Carlo trajectory with restraints like this: rmf = RMF.create_rmf_file('out.rmf') IMP.rmf.add_hierarchy(rmf, hierarchy) IMP.rmf.add_restraints(rmf, restraints) opt_state = IMP.rmf.SaveOptimizerState(model, rmf) opt_state.update_always("initial conformation") opt_state.set_period(10) my_score_function = IMP.core.RestraintsScoringFunction(restraints, "scoring function") o = IMP.core.MonteCarlo(model) o.add_optimizer_state(opt_state) o.set_scoring_function(my_score_function) Then I can nicely see the changes in the values of individual restraints using Chimera RMF viewer. But, I would like to see also how the my_score_function value changed over the optimization. Is it possible with IMP.rmf.SaveOptimizerState? Thanks in advance, Jan

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SAXS
by Georg Kempf 06 Jun '16

06 Jun '16

Hello, I am trying to combine crosslink restraints with SAXS data. I used an example script to generate a script that does the sampling with XL restraints and now I want to extend the script to test the models against the SAXS data by adding restraints e.g. radius of gyration, chi^2 value etc. I tried to use an example file but it does not really work after editing. My current problem is that I cannot load my SAXS data. I tried to use this function but it returns an error message: exp_profile = IMP.saxs.Profile.read_SAXS_file(datadirectory+'saxs.dat')) Does anyone know what's wrong here? Does anyone have other example scripts from which I can learn how to implement SAXS restraints together with XL restraints? Best, Georg

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ChimeraWriter
by Ibai Irastorza 06 Jun '16

06 Jun '16

Hello, Today I updated IMP to the last version (2.6.2) from 2.4 and I saw that IMP.display.ChimeraWriter does not exist anymore and rmf needs to be used to write the geometry to chimera format. I have been searching for examples and I think I need to use rmf_display and give "chimera" as a parameter, but I did not find any example, all the examples are with PymolWriter. Can anyone help me writing in chimera format using the rmf? And do I need to change more lines of code with this change or can I just replace "w = IMP.rmf.ChimeraWriter(storage_folder+"/"+chimera_file)" with a similar line?? thanks a lot Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa…

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