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274 discussions

Geometrical Transformations and their effects in written files
by Kai Karius 01 Jun '17

01 Jun '17

Dear all, this is my first mail on the list, so what I am going to do is: I) try what i am trying to achieve II) what classes/methods I use Its fairly simple: I create a molecule and endow it with some structure using the provided PMI classes: s = System() st = s.create_state() m = st.create_molecule(molecule.name ,sequence=molecule.get_sequence(),chain_id=molecule.chain_id) for pdb_path,chain_id in molecule: struc = m.add_structure(pdb_path,chain_id,soft_check=True) m.add_representation(struc,resolutions=[0]) The "molecule" object is a convenience class that holds the necessary information. The other methods and objects are typical pmi elements. I create a clone, build the system and decorate the clone because I want to apply a transformation to it. I do that, afterwards i write the system to pdb: c = m.create_clone(molecule.chain_id+"_C") s.build() cx = IMP.core.XYZ(c.get_hierarchy()) IMP.core.transform(cx,g) IMP.atom.write_pdb(s.get_hierarchy(),"test_1.pdb") g rotates the clone around some axis specified elsewhere. When I look at the file I would expect two molecule in different positions, yet they sit on top of each other. What am I missing? Thanks in advance and all the best, Kai (Jans friend)

2 1

IMP 2.7.0 release
by Ben Webb 13 Apr '17

13 Apr '17

IMP 2.7.0 is now available. This is a bugfix and major update release. Most notably we include a preview of mmCIF support for deposition of integrative models in PDB-dev (https://pdb-dev.rcsb.rutgers.edu/); see the IMP::pmi::mmcif module for more details. This release also includes a number of bug fixes and performance improvements. Note that this will be the last release that includes packages for RedHat Enterprise Linux 5 (and variants, such as CentOS 5), since RHEL 5 has reached end of life. See https://integrativemodeling.org/2.7.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ 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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Packing group of spheres
by Dushyant Sahoo 12 Apr '17

12 Apr '17

Dear users, I am new to IMP. I am trying to pack a group of spheres inside a box. The spheres inside each group have a fixed distance from its immediate neighboring spheres. I am able to pack spheres with the constraint that spheres inside a group have a minimum distance from all other spheres. I would be really grateful if somebody could help me with this as I have a deadline coming soon. Thank You, Dushyant Sahoo

2 1

RNA-protein crosslinking
by Genis Valentin 12 Apr '17

12 Apr '17

I would like to add a protein-RNA cross-link restraint to my representation. Is this possible at all in IMP? I tried to use a csv file similar to polii_juri.csv which is given in the IMP tutorial (https://integrativemodeling.org/2.6.2/doc/manual/rnapolii_stalk.html): prot1,res1,prot2,res2 RNA_component,345,protein_component,49 But this failes when I read it with IMP.pmi.restraints.crosslinking.ISDCrossLinkMS ISDCrossLinkMS: WARNING> residue 345 of chain RNA_component is not there Nevertheless, if I run: list_of_residues=[(345,"RNA_component")] for res in list_of_residues: particles=IMP.pmi.tools.select(representation,resolution=10,name=res[1],residue=res[0]) if len(particles)>1 : print(res[0],res[1],"more that one particle selected"); continue if len(particles)==0 : print (res[0],res[1],"no particle was selected"); continue print(res[0],res[1],IMP.core.XYZR(particles[0]).get_radius()) I get: 345 RNA_component 10.307014164455413 Thanks in advance! Genis

2 1

rmf trajectory
by Julian 12 Apr '17

12 Apr '17

Dear IMP, I ran ReplicaExchange on multiple CPU's with MPI and have all the rmfs and logs in the output dir. I would like to recreate the simulation trajectory in a single rmf in the order that the conformations were scored. Is there a way to dig that order information out of the log files somehow? Thanks, Julian

2 1

install from binaries on RHEL7
by Isabelle Phan 22 Feb '17

22 Feb '17

Hello I have an RHEL7 instance with epel-release-latest-7 installed. I downloaded the RHEL 7 IMP-mpich package from https://integrativemodeling.org/download-linux.html Installing with yum localinstall IMP-mpich-2.6.2-1.el7.centos.x86_64.rpm throws: Error: Package: IMP-mpich-2.6.2-1.el7.centos.x86_64 (/IMP-mpich-2.6.2-1.el7.centos.x86_64) Requires: IMP = 2.6.2-1.el7.centos How do I install the binaries? Isabelle

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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

4 3

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

2 1

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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