<div dir="ltr">so this is what is looks like with rmf_show:<div> </div><div><a href="https://gist.github.com/mysticvision/271d973806603967fd31">https://gist.github.com/mysticvision/271d973806603967fd31</a></div><div> </div><div>i'll email you the rmf now.</div><div> </div><div>thanks !</div><div><div class="gmail_extra"> <div class="gmail_quote">On 3 July 2014 14:28, <<a href="mailto:imp-users-request@salilab.org" target="_blank">imp-users-request@salilab.org</a>> wrote: <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Send IMP-users mailing list submissions to <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a> To subscribe or unsubscribe via the World Wide Web, visit <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> or, via email, send a message with subject or body 'help' to <a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a> You can reach the person managing the list at <a href="mailto:imp-users-owner@salilab.org">imp-users-owner@salilab.org</a> When replying, please edit your Subject line so it is more specific than "Re: Contents of IMP-users digest..." Today's Topics: 1. Re: Sampling and writing to pym/rmf (Josh Bullock) (Barak Raveh) ---------------------------------------------------------------------- Message: 1 Date: Thu, 3 Jul 2014 06:27:55 -0700 From: Barak Raveh <<a href="mailto:barak.raveh@gmail.com">barak.raveh@gmail.com</a>> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a>> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Josh Bullock) Message-ID: <<a href="mailto:CAHp%2B_UoKxFzCF8W21dQv5OhWFuSc78HZp8JdnBZH5eEjeNEEvQ@mail.gmail.com">CAHp+_UoKxFzCF8W21dQv5OhWFuSc78HZp8JdnBZH5eEjeNEEvQ@mail.gmail.com</a>> Content-Type: text/plain; charset="utf-8" You can use rmf_show and rmf_show -v to view your file in human readable format <a href="http://integrativemodeling.org/rmf/nightly/doc/executables.html" target="_blank">http://integrativemodeling.org/rmf/nightly/doc/executables.html</a> About chimera, are you using a latest nightly build? You can send me the RMF file and I'll give a look to see if it depends on the chimera version. Barak On Thu, Jul 3, 2014 at 5:55 AM, Josh Bullock <<a href="mailto:jma.bullock@gmail.com">jma.bullock@gmail.com</a>> wrote: > oh so there is something in the .rmf file, looks a bit garbled though ... > is this normal ? > > <a href="https://gist.github.com/mysticvision/271d973806603967fd31" target="_blank">https://gist.github.com/mysticvision/271d973806603967fd31</a> > > > On 3 July 2014 13:44, <<a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a>> wrote: > >> Send IMP-users mailing list submissions to >> <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> or, via email, send a message with subject or body 'help' to >> <a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a> >> >> You can reach the person managing the list at >> <a href="mailto:imp-users-owner@salilab.org">imp-users-owner@salilab.org</a> >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of IMP-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Sampling and writing to pym/rmf (Barak Raveh) (Josh Bullock) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 3 Jul 2014 13:44:22 +0100 >> From: Josh Bullock <<a href="mailto:jma.bullock@gmail.com">jma.bullock@gmail.com</a>> >> To: <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh) >> Message-ID: >> <CAHh_40_zsUCt4= >> <a href="mailto:nZbvDRd0owHzz_v_DHEiB-R%2BEm3ggDScS2zg@mail.gmail.com">nZbvDRd0owHzz_v_DHEiB-R+Em3ggDScS2zg@mail.gmail.com</a>> >> Content-Type: text/plain; charset="utf-8" >> >> aha okay, so now i'm generating .rmf files however when trying to open >> them >> in chimera I get the following error: >> >> "Invalid handle returned from H5Fopen(name.c_str(), H5F_ACC_RDONLY, >> plist)" >> in file " >> >> I'm not sure whether this is because I've created empty .rmf files or >> something else is wrong ... >> >> the code for making the rmf files: >> >> for i in range(0, cs.get_number_of_configurations()): >> cs.load_configuration(i) >> h = IMP.atom.Hierarchy.get_children(all) >> tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf") >> print "file is", tfn >> rh = RMF.create_rmf_file(tfn) >> >> # add the hierarchy to the file >> IMP.rmf.add_hierarchies(rh, h) >> >> # add the current configuration to the file as frame 0 >> IMP.rmf.save_frame(rh) >> >> >> On 3 July 2014 00:20, <<a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a>> wrote: >> >> > Send IMP-users mailing list submissions to >> > <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a> >> > >> > To subscribe or unsubscribe via the World Wide Web, visit >> > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > or, via email, send a message with subject or body 'help' to >> > <a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a> >> > >> > You can reach the person managing the list at >> > <a href="mailto:imp-users-owner@salilab.org">imp-users-owner@salilab.org</a> >> > >> > When replying, please edit your Subject line so it is more specific >> > than "Re: Contents of IMP-users digest..." >> > >> > >> > Today's Topics: >> > >> > 1. Re: Sampling and writing to pym/rmf (Barak Raveh) >> > >> > >> > ---------------------------------------------------------------------- >> > >> > Message: 1 >> > Date: Wed, 2 Jul 2014 16:20:19 -0700 >> > From: Barak Raveh <<a href="mailto:barak.raveh@gmail.com">barak.raveh@gmail.com</a>> >> > To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a>> >> > Subject: Re: [IMP-users] Sampling and writing to pym/rmf >> > Message-ID: >> > < >> > <a href="mailto:CAHp%2B_Uoq-HAyca9AX_pFcEje32ke3J3KuKZWYfuj%2BM8SZWUkCw@mail.gmail.com">CAHp+_Uoq-HAyca9AX_pFcEje32ke3J3KuKZWYfuj+M8SZWUkCw@mail.gmail.com</a>> >> > Content-Type: text/plain; charset="utf-8" >> > >> > Hi Josh, >> > >> > An IMP model contains a list of particles that are tightly associated >> with >> > it (a particle does not exist outside the context of a model). Given the >> > disclaimer that I have never used ConfigurationSet, my understanding >> from >> > its documentation is that when you load a configuration, the values of >> the >> > particles within the model are updated accordingly. If I understand your >> > code correctly, 'all' is the root of the hierarchy in your model, so it >> is >> > 'all' that you should add to the rmf. The values of 'all' and all of its >> > children are supposed to update when you load a configuration, >> > automatically. >> > >> > All that being said said - use this advice at own risk, perhaps someone >> > could advise you better. Let me know if you have more questions. >> > >> > Barak >> > >> > >> > On Wed, Jul 2, 2014 at 3:42 PM, Josh Bullock <<a href="mailto:jma.bullock@gmail.com">jma.bullock@gmail.com</a>> >> > wrote: >> > >> > > >> > > >> > > Conceptually I do ( i think ... ) but not practically. I'm hoping to >> view >> > > each of the models i created - with MSrestraints - separately as an >> .rmf >> > in >> > > chimera, just so i can see what i'm making ! >> > > >> > > so i have created my models using: >> > > >> > > cs= get_conformations(m) >> > > >> > > do i have to assign each model to a particle before i can write it to >> an >> > > .rmf ? Or is each model already a particle with hierarchy ? >> > > >> > > ------------------------------------------- >> > > >> > > for i in range(0, cs.get_number_of_configurations()): >> > > cs.load_configuration(i) >> > > h = IMP.atom.Hierarchy(m) # <------- how do i call the >> hierarchy >> > of >> > > the current loaded configuration ? >> > > c = p.get_children(h) >> > > tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf") >> > > rh = RMF.create_rmf_file(tfn) >> > > >> > > # add the hierarchy to the file >> > > IMP.rmf.add_hierarchies(rh, h) >> > > >> > > # add the current configuration to the file as frame 0 >> > > IMP.rmf.save_frame(rh) >> > > >> > > On 2 July 2014 23:03, <<a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a>> wrote: >> > > >> > >> Send IMP-users mailing list submissions to >> > >> <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a> >> > >> >> > >> To subscribe or unsubscribe via the World Wide Web, visit >> > >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> or, via email, send a message with subject or body 'help' to >> > >> <a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a> >> > >> >> > >> You can reach the person managing the list at >> > >> <a href="mailto:imp-users-owner@salilab.org">imp-users-owner@salilab.org</a> >> > >> >> > >> When replying, please edit your Subject line so it is more specific >> > >> than "Re: Contents of IMP-users digest..." >> > >> >> > >> >> > >> Today's Topics: >> > >> >> > >> 1. Re: Sampling and writing to pym/rmf (Barak Raveh) >> > >> >> > >> >> > >> >> ---------------------------------------------------------------------- >> > >> >> > >> Message: 1 >> > >> Date: Wed, 2 Jul 2014 15:03:19 -0700 >> > >> >> > >> From: Barak Raveh <<a href="mailto:barak.raveh@gmail.com">barak.raveh@gmail.com</a>> >> > >> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a>> >> > >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf >> > >> Message-ID: >> > >> <CAHp+_UqO8rXRMsUSndbg-c0jyDxnswDe9aFKvW889gGMU= >> > >> <a href="mailto:4MMQ@mail.gmail.com">4MMQ@mail.gmail.com</a>> >> > >> Content-Type: text/plain; charset="utf-8" >> > >> >> > >> >> > >> * I meant >> > >> >> > >> h = IMP.atom.Hierarchy(p) >> > >> c = p.get_children(h) >> > >> >> > >> this assumes that particle p was already decorated as Hierarchy (let >> me >> > >> know if you are not familiar with decorators, Hierarchy, or >> Particle). >> > >> >> > >> >> > >> >> > >> On Wed, Jul 2, 2014 at 3:02 PM, Barak Raveh <<a href="mailto:barak.raveh@gmail.com">barak.raveh@gmail.com</a>> >> > >> wrote: >> > >> >> > >> > Hi Josh, >> > >> > >> > >> > I think get_children() is only a member function of Hierarchy, so >> you >> > >> > should do something like >> > >> > >> > >> > IMP.atom.Hierarchy(p) >> > >> > c = p.get_children() >> > >> > >> > >> > 'cs' seems to be a ConfigurationSet object - are you sure that you >> > >> expect >> > >> > it to have children? >> > >> > >> > >> > What do you want to do? >> > >> > >> > >> > Cheers, >> > >> > Barak >> > >> > >> > >> > On Wed, Jul 2, 2014 at 1:42 PM, Josh Bullock < >> <a href="mailto:jma.bullock@gmail.com">jma.bullock@gmail.com</a>> >> > >> > wrote: >> > >> > >> > >> >> ah sorry ! this line gives me the error >> > >> >> >> > >> >> h= IMP.atom.Hierarchy.get_children(cs) >> > >> >> >> > >> >> thanks >> > >> >> >> > >> >> josh >> > >> >> >> > >> >> On 2 July 2014 17:45, <<a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a>> wrote: >> > >> >> >> > >> >>> Send IMP-users mailing list submissions to >> > >> >>> <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a> >> > >> >>> >> > >> >>> To subscribe or unsubscribe via the World Wide Web, visit >> > >> >>> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >>> or, via email, send a message with subject or body 'help' to >> > >> >>> <a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a> >> > >> >>> >> > >> >>> You can reach the person managing the list at >> > >> >>> <a href="mailto:imp-users-owner@salilab.org">imp-users-owner@salilab.org</a> >> > >> >>> >> > >> >>> When replying, please edit your Subject line so it is more >> specific >> > >> >>> than "Re: Contents of IMP-users digest..." >> > >> >>> >> > >> >>> >> > >> >>> Today's Topics: >> > >> >>> >> > >> >>> 1. Re: Sampling and writing to pym/rmf (Barak Raveh) (Barak >> > Raveh) >> > >> >>> >> > >> >>> >> > >> >>> >> > ---------------------------------------------------------------------- >> > >> >>> >> > >> >>> Message: 1 >> > >> >>> Date: Wed, 2 Jul 2014 09:45:30 -0700 >> > >> >>> From: Barak Raveh <<a href="mailto:barak.raveh@gmail.com">barak.raveh@gmail.com</a>> >> > >> >>> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a>> >> > >> >>> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak >> > Raveh) >> > >> >>> Message-ID: >> > >> >>> <CAHp+_Uo19VasJDJYi+2CoUUu= >> > >> >>> <a href="mailto:u_6duKCraVetU4dW45%2BoDhTAw@mail.gmail.com">u_6duKCraVetU4dW45+oDhTAw@mail.gmail.com</a>> >> > >> >>> Content-Type: text/plain; charset="utf-8" >> > >> >>> >> > >> >>> Which lines throws the error? >> > >> >>> >> > >> >>> >> > >> >>> On Wed, Jul 2, 2014 at 4:56 AM, Josh Bullock < >> <a href="mailto:jma.bullock@gmail.com">jma.bullock@gmail.com</a> >> > > >> > >> >>> wrote: >> > >> >>> >> > >> >>> > Hi Barek, >> > >> >>> > >> > >> >>> > So I'm not giving hierarchy.get_children the correct input: >> > >> >>> > >> > >> >>> > TypeError: unbound method get_children() must be called with >> > >> Hierarchy >> > >> >>> > instance as first argument (got ConfigurationSet instance >> instead) >> > >> >>> > >> > >> >>> > I'm not sure which argument is the hierarchy instance. >> > >> >>> > >> > >> >>> > Thanks, >> > >> >>> > >> > >> >>> > Josh >> > >> >>> > >> > >> >>> > ------------------------------------------------- >> > >> >>> > >> > >> >>> > cs= get_conformations(m) >> > >> >>> >> > >> >>> > >> > >> >>> > for i in range(0, cs.get_number_of_configurations()): >> > >> >>> > JOSH = cs.load_configuration(i) >> > >> >>> > S= IMP.atom.Selection >> > >> >>> > h= IMP.atom.Hierarchy.get_children(cs) >> > >> >>> > tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf") >> > >> >>> > rh = RMF.create_rmf_file(tfn) >> > >> >>> > >> > >> >>> > On 1 July 2014 17:31, <<a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a>> wrote: >> > >> >>> > >> > >> >>> >> Send IMP-users mailing list submissions to >> > >> >>> >> <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a> >> > >> >>> >> >> > >> >>> >> To subscribe or unsubscribe via the World Wide Web, visit >> > >> >>> >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >>> >> or, via email, send a message with subject or body 'help' to >> > >> >>> >> <a href="mailto:imp-users-request@salilab.org">imp-users-request@salilab.org</a> >> > >> >>> >> >> > >> >>> >> You can reach the person managing the list at >> > >> >>> >> <a href="mailto:imp-users-owner@salilab.org">imp-users-owner@salilab.org</a> >> > >> >>> >> >> > >> >>> >> When replying, please edit your Subject line so it is more >> > specific >> > >> >>> >> than "Re: Contents of IMP-users digest..." >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> Today's Topics: >> > >> >>> >> >> > >> >>> >> 1. Re: Sampling and writing to pym/rmf (Barak Raveh) >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > >> >> ---------------------------------------------------------------------- >> > >> >>> >> >> > >> >>> >> Message: 1 >> > >> >>> >> Date: Tue, 1 Jul 2014 09:31:33 -0700 >> > >> >>> >> From: Barak Raveh <<a href="mailto:barak.raveh@gmail.com">barak.raveh@gmail.com</a>> >> > >> >>> >> To: Help and discussion for users of IMP < >> <a href="mailto:imp-users@salilab.org">imp-users@salilab.org</a>> >> > >> >>> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf >> > >> >>> >> Message-ID: >> > >> >>> >> <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ= >> > >> >>> >> <a href="mailto:LvYPnJh-LjpC2cSA@mail.gmail.com">LvYPnJh-LjpC2cSA@mail.gmail.com</a>> >> > >> >>> >> Content-Type: text/plain; charset="utf-8" >> > >> >>> >> > >> >>> >> >> > >> >>> >> Hi Josh, from a very superficial look, your code to write the >> RMF >> > >> >>> files >> > >> >>> >> seems fine - do you get an output RMF file? Could you load it >> in >> > >> >>> Chimera? >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> On Tue, Jul 1, 2014 at 2:40 AM, Josh Bullock < >> > >> <a href="mailto:jma.bullock@gmail.com">jma.bullock@gmail.com</a>> >> > >> >>> >> wrote: >> > >> >>> >> >> > >> >>> >> > Hello, >> > >> >>> >> > >> > >> >>> >> > I'm relatively new to all this so please let me know if i'm >> > >> making >> > >> >>> any >> > >> >>> >> > obvious errors ... >> > >> >>> >> > >> > >> >>> >> > Essentially all i'm trying to do is generate an ensemble of >> > >> models >> > >> >>> made >> > >> >>> >> > from four subunits - constrained by MS connectivity >> restraints. >> > >> The >> > >> >>> >> models >> > >> >>> >> > get scored but nothing seems to write to the pymol file. >> > Ideally >> > >> i'd >> > >> >>> >> like >> > >> >>> >> > to write to an .rmf but i haven't worked that one out either >> > ... >> > >> >>> >> > >> > >> >>> >> > Is this a reasonable way to go about my problem ? >> > >> >>> >> > >> > >> >>> >> > Many thanks, >> > >> >>> >> > >> > >> >>> >> > Josh >> > >> >>> >> > >> > >> >>> >> > ------------------------------------------- >> > >> >>> >> > >> > >> >>> >> > import IMP >> > >> >>> >> > import IMP.atom >> > >> >>> >> > import IMP.rmf >> > >> >>> >> > import inspect >> > >> >>> >> > import IMP.container >> > >> >>> >> > import IMP.display >> > >> >>> >> > import IMP.statistics >> > >> >>> >> > #import IMP.example >> > >> >>> >> > import sys, math, os, optparse >> > >> >>> >> > import RMF >> > >> >>> >> > >> > >> >>> >> > from optparse import OptionParser >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> > # Convert the arguments into strings and number >> > >> >>> >> > Firstpdb = str(sys.argv[1]) >> > >> >>> >> > Secondpdb = str(sys.argv[2]) >> > >> >>> >> > Thirdpdb = str(sys.argv[3]) >> > >> >>> >> > Fourthpdb = str(sys.argv[4]) >> > >> >>> >> > models = float(sys.argv[5]) >> > >> >>> >> > >> > >> >>> >> > #***************************************** >> > >> >>> >> > >> > >> >>> >> > # the spring constant to use, it doesnt really matter >> > >> >>> >> > k=100 >> > >> >>> >> > # the target resolution for the representation, this is >> used to >> > >> >>> specify >> > >> >>> >> > how detailed >> > >> >>> >> > # the representation used should be >> > >> >>> >> > resolution=300 >> > >> >>> >> > # the box to perform everything >> > >> >>> >> > bb=IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0,0,0), >> > >> >>> >> > IMP.algebra.Vector3D(300, 300, >> > 300)) >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> > # this function creates the molecular hierarchies for the >> > various >> > >> >>> >> involved >> > >> >>> >> > proteins >> > >> >>> >> > def create_representation(): >> > >> >>> >> > m= IMP.Model() >> > >> >>> >> > all=IMP.atom.Hierarchy.setup_particle(IMP.Particle(m)) >> > >> >>> >> > all.set_name("the universe") >> > >> >>> >> > # create a protein, represented as a set of connected >> balls >> > >> of >> > >> >>> >> > appropriate >> > >> >>> >> > # radii and number, chose by the resolution parameter >> and >> > the >> > >> >>> >> number of >> > >> >>> >> > # amino acids. >> > >> >>> >> > >> > >> >>> >> > def create_protein_from_pdbs(name, files): >> > >> >>> >> > >> > >> >>> >> > def create_from_pdb(file): >> > >> >>> >> > sls=IMP.SetLogState(IMP.NONE) >> > >> >>> >> > datadir = os.getcwd() >> > >> >>> >> > print datadir >> > >> >>> >> > t=IMP.atom.read_pdb( datadir+'/' + file, m, >> > >> >>> >> > IMP.atom.ATOMPDBSelector()) >> > >> >>> >> > del sls >> > >> >>> >> > #IMP.atom.show_molecular_hierarchy(t) >> > >> >>> >> > c=IMP.atom.Chain(IMP.atom.get_by_type(t, >> > >> >>> >> > IMP.atom.CHAIN_TYPE)[0]) >> > >> >>> >> > if c.get_number_of_children()==0: >> > >> >>> >> > IMP.atom.show_molecular_hierarchy(t) >> > >> >>> >> > # there is no reason to use all atoms, just >> > >> approximate >> > >> >>> the >> > >> >>> >> > pdb shape instead >> > >> >>> >> > s=IMP.atom.create_simplified_along_backbone(c, >> > >> >>> >> > >> > >> >>> >> resolution/300.0) >> > >> >>> >> > IMP.atom.destroy(t) >> > >> >>> >> > # make the simplified structure rigid >> > >> >>> >> > rb=IMP.atom.create_rigid_body(s) >> > >> >>> >> > # rb=IMP.atom.create_rigid_body(c) >> > >> >>> >> > rb.set_coordinates_are_optimized(True) >> > >> >>> >> > return s >> > >> >>> >> > # return c >> > >> >>> >> > >> > >> >>> >> > h= create_from_pdb(files[0]) >> > >> >>> >> > h.set_name(name) >> > >> >>> >> > all.add_child(h) >> > >> >>> >> > >> > >> >>> >> > create_protein_from_pdbs("A", [Firstpdb]) >> > >> >>> >> > create_protein_from_pdbs("B", [Secondpdb]) >> > >> >>> >> > create_protein_from_pdbs("C", [Thirdpdb]) >> > >> >>> >> > create_protein_from_pdbs("D", [Fourthpdb]) >> > >> >>> >> > #create_protein_from_pdbs("C", ["rpt3_imp.pdb"]) >> > >> >>> >> > return (m, all) >> > >> >>> >> > >> > >> >>> >> > # create the needed restraints and add them to the model >> > >> >>> >> > >> > >> >>> >> > def create_restraints(m, all): >> > >> >>> >> > def add_connectivity_restraint(s): >> > >> >>> >> > >> > >> >>> >> > tr= IMP.core.TableRefiner() >> > >> >>> >> > rps=[] >> > >> >>> >> > for sc in s: >> > >> >>> >> > ps= sc.get_selected_particles() >> > >> >>> >> > rps.append(ps[0]) >> > >> >>> >> > tr.add_particle(ps[0], ps) >> > >> >>> >> > >> > >> >>> >> > # duplicate the >> IMP.atom.create_connectivity_restraint >> > >> >>> >> > functionality >> > >> >>> >> > >> > >> >>> >> > score= >> > >> >>> >> > >> > >> >>> >> >> > >> >>> >> > >> >> > >> IMP.core.KClosePairsPairScore(IMP.core.HarmonicSphereDistancePairScore(0,1),tr) >> > >> >>> >> > >> > >> >>> >> > r= IMP.core.MSConnectivityRestraint(m,score) >> > >> >>> >> > >> > >> >>> >> > iA = r.add_type([rps[0]]) >> > >> >>> >> > iB = r.add_type([rps[1]]) >> > >> >>> >> > iC = r.add_type([rps[2]]) >> > >> >>> >> > iD = r.add_type([rps[3]]) >> > >> >>> >> > n1 = r.add_composite([iA, iB, iC, iD]) >> > >> >>> >> > n2 = r.add_composite([iA, iB], n1) >> > >> >>> >> > n3 = r.add_composite([iC, iD], n1) >> > >> >>> >> > n4 = r.add_composite([iB, iC, iD], n1) >> > >> >>> >> > >> > >> >>> >> > m.add_restraint(r) >> > >> >>> >> > >> > >> >>> >> > evr=IMP.atom.create_excluded_volume_restraint([all]) >> > >> >>> >> > m.add_restraint(evr) >> > >> >>> >> > # a Selection allows for natural specification of what >> the >> > >> >>> >> restraints >> > >> >>> >> > act on >> > >> >>> >> > S= IMP.atom.Selection >> > >> >>> >> > sA=S(hierarchy=all, molecule="A") >> > >> >>> >> > sB=S(hierarchy=all, molecule="B") >> > >> >>> >> > sC=S(hierarchy=all, molecule="C") >> > >> >>> >> > sD=S(hierarchy=all, molecule="D") >> > >> >>> >> > add_connectivity_restraint([sA, sB, sC, sD]) >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> > # find acceptable conformations of the model >> > >> >>> >> > def get_conformations(m): >> > >> >>> >> > sampler= IMP.core.MCCGSampler(m) >> > >> >>> >> > sampler.set_bounding_box(bb) >> > >> >>> >> > # magic numbers, experiment with them and make them >> large >> > >> >>> enough for >> > >> >>> >> > things to work >> > >> >>> >> > sampler.set_number_of_conjugate_gradient_steps(100) >> > >> >>> >> > sampler.set_number_of_monte_carlo_steps(20) >> > >> >>> >> > sampler.set_number_of_attempts(models) >> > >> >>> >> > # We don't care to see the output from the sampler >> > >> >>> >> > sampler.set_log_level(IMP.SILENT) >> > >> >>> >> > # return the IMP.ConfigurationSet storing all the found >> > >> >>> >> configurations >> > >> >>> >> > that >> > >> >>> >> > # meet the various restraint maximum scores. >> > >> >>> >> > cs= sampler.create_sample() >> > >> >>> >> > return cs >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> > # cluster the conformations and write them to a file >> > >> >>> >> > def analyze_conformations(cs, all, gs): >> > >> >>> >> > # we want to cluster the configurations to make them >> easier >> > >> to >> > >> >>> >> > understand >> > >> >>> >> > # in the case, the clustering is pretty meaningless >> > >> >>> >> > embed= IMP.statistics.ConfigurationSetXYZEmbedding(cs, >> > >> >>> >> > >> > >> >>> >> > >> > IMP.container.ListSingletonContainer(IMP.atom.get_leaves(all)), >> > >> >>> True) >> > >> >>> >> > cluster= IMP.statistics.create_lloyds_kmeans(embed, 10, >> > >> 10000) >> > >> >>> >> > # dump each cluster center to a file so it can be >> viewed. >> > >> >>> >> > for i in range(cluster.get_number_of_clusters()): >> > >> >>> >> > center= cluster.get_cluster_center(i) >> > >> >>> >> > cs.load_configuration(i) >> > >> >>> >> > w= IMP.display.PymolWriter("cluster.%d.pym"%i) >> > >> >>> >> > for g in gs: >> > >> >>> >> > w.add_geometry(g) >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> >> > >> >>> >> > >> >> > >> #****************************************************************************************** >> > >> >>> >> > # now do the actual work >> > >> >>> >> > >> > >> >>> >> > (m,all)= create_representation() >> > >> >>> >> > IMP.atom.show_molecular_hierarchy(all) >> > >> >>> >> > create_restraints(m, all) >> > >> >>> >> > >> > >> >>> >> > # in order to display the results, we need something that >> maps >> > >> the >> > >> >>> >> > particles onto >> > >> >>> >> > # geometric objets. The IMP.display.Geometry objects do this >> > >> >>> mapping. >> > >> >>> >> > # IMP.display.XYZRGeometry map an IMP.core.XYZR particle >> onto a >> > >> >>> sphere >> > >> >>> >> > gs=[] >> > >> >>> >> > for i in range(all.get_number_of_children()): >> > >> >>> >> > color= IMP.display.get_display_color(i) >> > >> >>> >> > n= all.get_child(i) >> > >> >>> >> > name= n.get_name() >> > >> >>> >> > g= IMP.atom.HierarchyGeometry(n) >> > >> >>> >> > g.set_color(color) >> > >> >>> >> > gs.append(g) >> > >> >>> >> > >> > >> >>> >> > cs= get_conformations(m) >> > >> >>> >> > >> > >> >>> >> > print "found", cs.get_number_of_configurations(), >> "solutions" >> > >> >>> >> > >> > >> >>> >> > ListScores = [] >> > >> >>> >> > for i in range(0, cs.get_number_of_configurations()): >> > >> >>> >> > cs.load_configuration(i) >> > >> >>> >> > # print the configuration >> > >> >>> >> > print "solution number: ",i,"scored :", >> > m.evaluate(False) >> > >> >>> >> > ListScores.append(m.evaluate(False)) >> > >> >>> >> > >> > >> >>> >> > f1 = open("out_scores.csv", "w") >> > >> >>> >> > f1.write("\n".join(map(lambda x: str(x), ListScores))) >> > >> >>> >> > f1.close() >> > >> >>> >> > >> > >> >>> >> > # for each of the configuration, dump it to a file to view >> in >> > >> pymol >> > >> >>> >> > for i in range(0, cs.get_number_of_configurations()): >> > >> >>> >> > JOSH = cs.load_configuration(i) >> > >> >>> >> > S= IMP.atom.Selection >> > >> >>> >> > h= IMP.atom.Hierarchy.get_children(cs) >> > >> >>> >> > tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf") >> > >> >>> >> > rh = RMF.create_rmf_file(tfn) >> > >> >>> >> > >> > >> >>> >> > # add the hierarchy to the file >> > >> >>> >> > IMP.rmf.add_hierarchies(rh, h) >> > >> >>> >> > >> > >> >>> >> > # add the current configuration to the file as frame 0 >> > >> >>> >> > IMP.rmf.save_frame(rh) >> > >> >>> >> > >> > >> >>> >> > for g in gs: >> > >> >>> >> > w.add_geometry(g) >> > >> >>> >> > >> > >> >>> >> > analyze_conformations(cs, all, gs) >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> > _______________________________________________ >> > >> >>> >> > IMP-users mailing list >> > >> >>> >> > <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > >> >>> >> > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >>> >> > >> > >> >>> >> > >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> -- >> > >> >>> >> Barak >> > >> >>> >> -------------- next part -------------- >> > >> >>> >> An HTML attachment was scrubbed... >> > >> >>> >> URL: < >> > >> >>> >> >> > >> >>> >> > >> >> > >> <a href="http://salilab.org/archives/imp-users/attachments/20140701/7b0e5f9f/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140701/7b0e5f9f/attachment.html</a> >> > >> >>> >> > >> > >> >>> >> >> > >> >>> >> ------------------------------ >> > >> >>> >> > >> >>> >> >> > >> >>> >> _______________________________________________ >> > >> >>> >> IMP-users mailing list >> > >> >>> >> <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > >> >>> >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> End of IMP-users Digest, Vol 38, Issue 2 >> > >> >>> >> **************************************** >> > >> >>> >> > >> >>> >> >> > >> >>> > >> > >> >>> > >> > >> >>> > _______________________________________________ >> > >> >>> > IMP-users mailing list >> > >> >>> > <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > >> >>> > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >>> > >> > >> >>> > >> > >> >>> >> > >> >>> >> > >> >>> -- >> > >> >>> Barak >> > >> >>> -------------- next part -------------- >> > >> >>> An HTML attachment was scrubbed... >> > >> >>> URL: < >> > >> >>> >> > >> >> > >> <a href="http://salilab.org/archives/imp-users/attachments/20140702/081e70ca/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140702/081e70ca/attachment.html</a> >> > >> >>> > >> > >> >>> >> > >> >>> ------------------------------ >> > >> >>> >> > >> >>> >> > >> >>> _______________________________________________ >> > >> >>> IMP-users mailing list >> > >> >>> <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > >> >>> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >>> >> > >> >>> >> > >> >>> End of IMP-users Digest, Vol 38, Issue 4 >> > >> >>> **************************************** >> > >> >>> >> > >> >> >> > >> >> >> > >> >> _______________________________________________ >> > >> >> IMP-users mailing list >> > >> >> <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > >> >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >> >> > >> >> >> > >> > >> > >> > >> > >> > -- >> > >> > Barak >> > >> > >> > >> >> > >> >> > >> >> > >> -- >> > >> Barak >> > >> -------------- next part -------------- >> > >> An HTML attachment was scrubbed... >> > >> URL: < >> > >> >> > >> <a href="http://salilab.org/archives/imp-users/attachments/20140702/74f552a1/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140702/74f552a1/attachment.html</a> >> > >> > >> > >> >> > >> >> > >> ------------------------------ >> > >> >> > >> _______________________________________________ >> > >> IMP-users mailing list >> > >> <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> >> > >> >> > >> End of IMP-users Digest, Vol 38, Issue 7 >> > >> **************************************** >> > >> >> > > >> > > >> > > _______________________________________________ >> > > IMP-users mailing list >> > > <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > > >> > > >> > >> > >> > -- >> > Barak >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: < >> > >> <a href="http://salilab.org/archives/imp-users/attachments/20140702/2f1fb30c/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140702/2f1fb30c/attachment.html</a> >> > > >> > >> > ------------------------------ >> > >> > _______________________________________________ >> > IMP-users mailing list >> > <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> > >> > >> > End of IMP-users Digest, Vol 38, Issue 9 >> > **************************************** >> > >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> <a href="http://salilab.org/archives/imp-users/attachments/20140703/fe3a183b/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140703/fe3a183b/attachment.html</a> >> > >> >> ------------------------------ >> >> _______________________________________________ >> IMP-users mailing list >> <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> >> >> >> End of IMP-users Digest, Vol 38, Issue 10 >> ***************************************** >> > > > _______________________________________________ > IMP-users mailing list > <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> > > -- Barak -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://salilab.org/archives/imp-users/attachments/20140703/ebc4da96/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140703/ebc4da96/attachment.html</a>> ------------------------------ _______________________________________________ IMP-users mailing list <a href="mailto:IMP-users@salilab.org">IMP-users@salilab.org</a> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a> End of IMP-users Digest, Vol 38, Issue 12 ***************************************** </blockquote></div> </div></div></div>