April 2011 - IMP-users

IMP.hdf5 changes
by Daniel Russel 22 Apr '11

22 Apr '11

As my initial naming scheme for the IMP methods in the hdf5 module seems to have confused everyone, I've changed it to a new, hopefully clearer, one. Sorry about the change, but I think it will make the model much easier to figure out. The new methods treat the files as objects rather than IO in light of the persistent state that is associated with them. Changes are - write_X -> add_X - save_configuration -> save_frame - load_configuration -> load_frame - read_all_X -> create_X To be more consistent with similarly named IMP methods, all methods take the RootHandle as the first argument. If they take a frame, it is the second argument. Hope this helps things. The module overview docs have been improved a bit too.

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Strange Pair Restraint behaviour
by Iain Moal 10 Apr '11

10 Apr '11

Hello IMP users, My pair restraints aren’t behaving as they should. I have a system with multiple domains which I want to move as rigid bodies while having a pair restraint between the end of the first domain and the beginning of the next. My input .pdb files are coarse-grained using IMP.atom.create_simplified_along_backbone. My approach was to take the coordinates of the alpha carbons I want to restrain, add the two points into my coarse-grained RigidBody objects, and add a pair restraint between them, see the following code. The funny thing is, as my initial .pdb files satisfy this restraint, an initial energy evaluation comes out as zero, as it should do. However, if I perturb the system and minimise with the MC mover, the energy starts high and reduces down to almost zero, as it should, but the distances between adjacent domains of the final structure are much higher than they should be – often over 20A away from the HarmonicUpperBound. I have set my_MC_optimiser.set_return_best(True), so this isn’t the reason. Does anyone have any idea what is wrong? Many thanks, Iain Moal Hingedata = [[9,0,34.885,-57.443,9.494,23.464,-48.297,6.885],… and so on] rigbods=[] for abcd in IMP.atom.get_by_type(all, IMP.atom.CHAIN_TYPE): rigbods.append(IMP.core.RigidBody(IMP.Decorator.get_particle(IMP.atom.Hierarchy.get_as_chain(abcd)))) for x in hingedata: p1 = IMP.Particle(m) p2 = IMP.Particle(m) XYZ_a= IMP.core.XYZR.setup_particle(p1,IMP.algebra.Sphere3D(IMP.algebra.Vector3D(x[2],x[3],x[4]),0.01)) XYZ_b= IMP.core.XYZR.setup_particle(p2,IMP.algebra.Sphere3D(IMP.algebra.Vector3D(x[5],x[6],x[7]),0.01)) #NB) THIS DOESN’T WORK HERE: XYZ_a= IMP.core.XYZ.setup_particle(p1,IMP.algebra.Vector3D(x[2],x[3],x[4])) # NB) THIS DOESN’T WORK HERE:XYZ_b= IMP.core.XYZ.setup_particle(p2,IMP.algebra.Vector3D(x[5],x[6],x[7])) rigbods[x[0]].add_member(XYZ_a) rigbods[x[1]].add_member(XYZ_b) r= IMP.core.PairRestraint(IMP.core.DistancePairScore(IMP.core.HarmonicUpperBound(20,5.0)),IMP.ParticlePair(p1,p2)) m.add_restraint(r) I read my .pdb files using this: all.add_child(create_from_pdb(“filename”)) def create_from_pdb(file): t=IMP.atom.read_pdb(file, m, IMP.atom.ATOMPDBSelector()) IMP.atom.add_radii(t) c=IMP.atom.Chain( IMP.Decorator.get_particle(IMP.atom.Hierarchy.get_as_chain(IMP.atom.get_by_type(t, IMP.atom.CHAIN_TYPE)[0] ))) s=IMP.atom.create_simplified_along_backbone(c,4) IMP.atom.destroy(t) IMP.Decorator.get_particle(IMP.atom.Hierarchy.get_as_chain(IMP.atom.get_by_type(s, IMP.atom.CHAIN_TYPE)[0] )) rb=IMP.atom.setup_as_rigid_body(s) rb.set_coordinates_are_optimized(True) return s This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

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Question about conditional restraints
by Davide Bau 04 Apr '11

04 Apr '11

Hi everyone, I need to implement a conditional restraint to account for multiple copies of the same particles in my data set, ie to account for interaction ambiguity. Are conditional restraints implemented in IMP? Thanks! Davide -- Davide Baù Structural Genomics Unit Bioinformatics & Genomics Department, Prince Felipe Research Center Avda. Autopista del Saler 16, 46012 Valencia, Spain Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 email: dbau(a)cipf.es web: http://bioinfo.cipf.es/dbau/

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a remark concerning chains in a hierarchy returned by read_pdb
by Benjamin SCHWARZ 04 Apr '11

04 Apr '11

Hi list, Using read_pdb, I expected it to return a hierarchy with distinct chains that could be plainly distinguished solely on their chain ID, this seems not to be the case, and I don't know wether this is a desired behavior or a minor bug. As an exemple, pdb structure '1pgu' contains : - two protein chains, A and B - two Zinc ions (one of them being attached to chain A and the other to chain B) - and water molecules attached to both chains. When read through read_pdb, the hierarchy contains 4 children, all 4 eligible for a "conversion" to Chain, each Zinc ion being considered as a chain. I thus have two chains A and two chains B in the hierarchy. --Ben.S.

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