November 2016 - IMP-users

Re: [IMP-users] SAXSISDRestaint
by Josh Bullock 01 Dec '16

01 Dec '16

okay thanks for the advice. Just trying to get SAXSRestraint working now ... I get the following error: > Profile is not sampled for q = 0.0054794, q_max = 0.5 > You can remove points with q > 0.5 from the experimental profile or > recompute the profile with higher max_q > I'm slightly confused as 0.0054795 < 0.5, and also there are no values in my .dat file above 0.5. Finally, there doesn't seem to be a way to alter the max_q through the pmi module, would i have to go through the C++ ? Thanks, josh

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SAXSISDRestaint
by Josh Bullock 30 Nov '16

30 Nov '16

hello imp users, I'm trying to use the pmi.SAXSISDRestraint to model with crosslinks and SAXS, ideally all in the ISD ReplicaExchange method, however it says I need isd2. Does this exist anywhere, or is the SAXS restraint not working in this capacity ? I tried using it regardless, but it asks for a representation. I'm not sure how to get the representation. I tried the system, state, model, molecule, root_hierarchy, molecule.get_represented() ... how do i get the representation ? any help greatly appreciated, thanks ! Josh

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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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