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Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh)
by Josh Bullock 03 Jul '14

03 Jul '14

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, <imp-users-request(a)salilab.org> wrote: > Send IMP-users mailing list submissions to > imp-users(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/imp-users > or, via email, send a message with subject or body 'help' to > imp-users-request(a)salilab.org > > You can reach the person managing the list at > imp-users-owner(a)salilab.org > > 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 <barak.raveh(a)gmail.com> > To: Help and discussion for users of IMP <imp-users(a)salilab.org> > Subject: Re: [IMP-users] Sampling and writing to pym/rmf > Message-ID: > < > CAHp+_Uoq-HAyca9AX_pFcEje32ke3J3KuKZWYfuj+M8SZWUkCw(a)mail.gmail.com> > 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 <jma.bullock(a)gmail.com> > 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, <imp-users-request(a)salilab.org> wrote: > > > >> Send IMP-users mailing list submissions to > >> imp-users(a)salilab.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://salilab.org/mailman/listinfo/imp-users > >> or, via email, send a message with subject or body 'help' to > >> imp-users-request(a)salilab.org > >> > >> You can reach the person managing the list at > >> imp-users-owner(a)salilab.org > >> > >> 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 <barak.raveh(a)gmail.com> > >> To: Help and discussion for users of IMP <imp-users(a)salilab.org> > >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf > >> Message-ID: > >> <CAHp+_UqO8rXRMsUSndbg-c0jyDxnswDe9aFKvW889gGMU= > >> 4MMQ(a)mail.gmail.com> > >> 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 <barak.raveh(a)gmail.com> > >> 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 <jma.bullock(a)gmail.com> > >> > wrote: > >> > > >> >> ah sorry ! this line gives me the error > >> >> > >> >> h= IMP.atom.Hierarchy.get_children(cs) > >> >> > >> >> thanks > >> >> > >> >> josh > >> >> > >> >> On 2 July 2014 17:45, <imp-users-request(a)salilab.org> wrote: > >> >> > >> >>> Send IMP-users mailing list submissions to > >> >>> imp-users(a)salilab.org > >> >>> > >> >>> To subscribe or unsubscribe via the World Wide Web, visit > >> >>> https://salilab.org/mailman/listinfo/imp-users > >> >>> or, via email, send a message with subject or body 'help' to > >> >>> imp-users-request(a)salilab.org > >> >>> > >> >>> You can reach the person managing the list at > >> >>> imp-users-owner(a)salilab.org > >> >>> > >> >>> 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 <barak.raveh(a)gmail.com> > >> >>> To: Help and discussion for users of IMP <imp-users(a)salilab.org> > >> >>> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak > Raveh) > >> >>> Message-ID: > >> >>> <CAHp+_Uo19VasJDJYi+2CoUUu= > >> >>> u_6duKCraVetU4dW45+oDhTAw(a)mail.gmail.com> > >> >>> Content-Type: text/plain; charset="utf-8" > >> >>> > >> >>> Which lines throws the error? > >> >>> > >> >>> > >> >>> On Wed, Jul 2, 2014 at 4:56 AM, Josh Bullock <jma.bullock(a)gmail.com > > > >> >>> 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, <imp-users-request(a)salilab.org> wrote: > >> >>> > > >> >>> >> Send IMP-users mailing list submissions to > >> >>> >> imp-users(a)salilab.org > >> >>> >> > >> >>> >> To subscribe or unsubscribe via the World Wide Web, visit > >> >>> >> https://salilab.org/mailman/listinfo/imp-users > >> >>> >> or, via email, send a message with subject or body 'help' to > >> >>> >> imp-users-request(a)salilab.org > >> >>> >> > >> >>> >> You can reach the person managing the list at > >> >>> >> imp-users-owner(a)salilab.org > >> >>> >> > >> >>> >> 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 <barak.raveh(a)gmail.com> > >> >>> >> To: Help and discussion for users of IMP <imp-users(a)salilab.org> > >> >>> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf > >> >>> >> Message-ID: > >> >>> >> <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ= > >> >>> >> LvYPnJh-LjpC2cSA(a)mail.gmail.com> > >> >>> >> 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 < > >> jma.bullock(a)gmail.com> > >> >>> >> 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 > >> >>> >> > IMP-users(a)salilab.org > >> >>> >> > https://salilab.org/mailman/listinfo/imp-users > >> >>> >> > > >> >>> >> > > >> >>> >> > >> >>> >> > >> >>> >> -- > >> >>> >> Barak > >> >>> >>

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Re: [IMP-users] Sampling and writing to pym/rmf
by Josh Bullock 02 Jul '14

02 Jul '14

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, <imp-users-request(a)salilab.org> wrote: > Send IMP-users mailing list submissions to > imp-users(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/imp-users > or, via email, send a message with subject or body 'help' to > imp-users-request(a)salilab.org > > You can reach the person managing the list at > imp-users-owner(a)salilab.org > > 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 <barak.raveh(a)gmail.com> > To: Help and discussion for users of IMP <imp-users(a)salilab.org> > Subject: Re: [IMP-users] Sampling and writing to pym/rmf > Message-ID: > <CAHp+_UqO8rXRMsUSndbg-c0jyDxnswDe9aFKvW889gGMU= > 4MMQ(a)mail.gmail.com> > 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 <barak.raveh(a)gmail.com> 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 <jma.bullock(a)gmail.com> > > wrote: > > > >> ah sorry ! this line gives me the error > >> > >> h= IMP.atom.Hierarchy.get_children(cs) > >> > >> thanks > >> > >> josh > >> > >> On 2 July 2014 17:45, <imp-users-request(a)salilab.org> wrote: > >> > >>> Send IMP-users mailing list submissions to > >>> imp-users(a)salilab.org > >>> > >>> To subscribe or unsubscribe via the World Wide Web, visit > >>> https://salilab.org/mailman/listinfo/imp-users > >>> or, via email, send a message with subject or body 'help' to > >>> imp-users-request(a)salilab.org > >>> > >>> You can reach the person managing the list at > >>> imp-users-owner(a)salilab.org > >>> > >>> 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 <barak.raveh(a)gmail.com> > >>> To: Help and discussion for users of IMP <imp-users(a)salilab.org> > >>> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh) > >>> Message-ID: > >>> <CAHp+_Uo19VasJDJYi+2CoUUu= > >>> u_6duKCraVetU4dW45+oDhTAw(a)mail.gmail.com> > >>> Content-Type: text/plain; charset="utf-8" > >>> > >>> Which lines throws the error? > >>> > >>> > >>> On Wed, Jul 2, 2014 at 4:56 AM, Josh Bullock <jma.bullock(a)gmail.com> > >>> 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, <imp-users-request(a)salilab.org> wrote: > >>> > > >>> >> Send IMP-users mailing list submissions to > >>> >> imp-users(a)salilab.org > >>> >> > >>> >> To subscribe or unsubscribe via the World Wide Web, visit > >>> >> https://salilab.org/mailman/listinfo/imp-users > >>> >> or, via email, send a message with subject or body 'help' to > >>> >> imp-users-request(a)salilab.org > >>> >> > >>> >> You can reach the person managing the list at > >>> >> imp-users-owner(a)salilab.org > >>> >> > >>> >> 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 <barak.raveh(a)gmail.com> > >>> >> To: Help and discussion for users of IMP <imp-users(a)salilab.org> > >>> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf > >>> >> Message-ID: > >>> >> <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ= > >>> >> LvYPnJh-LjpC2cSA(a)mail.gmail.com> > >>> >> 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 <jma.bullock(a)gmail.com > > > >>> >> 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 > >>> >> > IMP-users(a)salilab.org > >>> >> > https://salilab.org/mailman/listinfo/imp-users > >>> >> > > >>> >> > > >>> >> > >>> >> > >>> >> -- > >>> >> Barak > >>> >>

2 1

Re: [IMP-users] Sampling and writing to pym/rmf
by Josh Bullock 02 Jul '14

02 Jul '14

ah sorry ! this line gives me the error h= IMP.atom.Hierarchy.get_children(cs) thanks josh On 2 July 2014 17:45, <imp-users-request(a)salilab.org> wrote: > Send IMP-users mailing list submissions to > imp-users(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/imp-users > or, via email, send a message with subject or body 'help' to > imp-users-request(a)salilab.org > > You can reach the person managing the list at > imp-users-owner(a)salilab.org > > 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 <barak.raveh(a)gmail.com> > To: Help and discussion for users of IMP <imp-users(a)salilab.org> > Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh) > Message-ID: > <CAHp+_Uo19VasJDJYi+2CoUUu= > u_6duKCraVetU4dW45+oDhTAw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Which lines throws the error? > > > On Wed, Jul 2, 2014 at 4:56 AM, Josh Bullock <jma.bullock(a)gmail.com> > 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, <imp-users-request(a)salilab.org> wrote: > > > >> Send IMP-users mailing list submissions to > >> imp-users(a)salilab.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://salilab.org/mailman/listinfo/imp-users > >> or, via email, send a message with subject or body 'help' to > >> imp-users-request(a)salilab.org > >> > >> You can reach the person managing the list at > >> imp-users-owner(a)salilab.org > >> > >> 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 <barak.raveh(a)gmail.com> > >> To: Help and discussion for users of IMP <imp-users(a)salilab.org> > >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf > >> Message-ID: > >> <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ= > >> LvYPnJh-LjpC2cSA(a)mail.gmail.com> > >> 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 <jma.bullock(a)gmail.com> > >> 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 > >> > IMP-users(a)salilab.org > >> > https://salilab.org/mailman/listinfo/imp-users > >> > > >> > > >> > >> > >> -- > >> Barak > >>

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Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh)
by Josh Bullock 02 Jul '14

02 Jul '14

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, <imp-users-request(a)salilab.org> wrote: > Send IMP-users mailing list submissions to > imp-users(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/imp-users > or, via email, send a message with subject or body 'help' to > imp-users-request(a)salilab.org > > You can reach the person managing the list at > imp-users-owner(a)salilab.org > > 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 <barak.raveh(a)gmail.com> > To: Help and discussion for users of IMP <imp-users(a)salilab.org> > Subject: Re: [IMP-users] Sampling and writing to pym/rmf > Message-ID: > <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ= > LvYPnJh-LjpC2cSA(a)mail.gmail.com> > 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 <jma.bullock(a)gmail.com> > 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 > > IMP-users(a)salilab.org > > https://salilab.org/mailman/listinfo/imp-users > > > > > > > -- > Barak >

2 1

Sampling and writing to pym/rmf
by Josh Bullock 01 Jul '14

01 Jul '14

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)

3 2

problem in installing IMP
by Pooja Dnyane 25 Jun '14

25 Jun '14

Hello sir/ mam, I want to install IMP but, somehow while compilation of code in IMP directory when I enter the "make j4" command it stops after 37% is complete. I tried different values for j e.g. 8 but again same error occurred.

2 1

problems when using multifit
by Fiona Bridget Naughton 05 Jun '14

05 Jun '14

Hi all, I'm trying to use the multifit application on a system with multiple copies of some subunits, but I'm having a couple of problems: 1. I keep getting solutions in which the subunits are overlapping, with identical subunits in exactly (or close to) the same place, leaving empty space elsewhere in the map. If I reduce the max penetration allowed/increase the penetration coefficient, I get no solutions. Are there any other parameters I should try changing? (It's not at all clear what many of the parameters in the alignment.param file are for, so I don't know which others might be relevant). Or anything else I could do? 2. I would like to define x-links involving the subunits with multiple copies, but the multifit application currently doesn't support ambiguity for cross-links. I was planning to modify ProteomicsEMAlignmentAtomics's add_all_restraints() method to add x-links as ConnectivityRestraints instead, but I'm not sure how/where to introduce these changes. Editing the .h/.cpp files in my folder has no effect, and I get errors when changing multifit's __init__.py due to various functions/classes not being defined (they're imported to the .h/.cpp file instead of defined in __init__). I know little about python/c++ beyond syntax, so I may be going about this the wrong way. Do I need to be doing something involving swig? Or something else? Any help will be greatly appreciated! Thanks, - Fiona

2 1

(no subject)
by Joseph Eschweiler 21 May '14

21 May '14

Hello, I just upgraded from 2.0 to 2.2 and now encounter an error that I'm unable to fix. File "angle.py", line 64, in get_conformations cs = sampler.create_sample() File "/usr/lib64/python2.6/site-packages/IMP/kernel/__init__.py", line 4106, in create_sample return _IMP_kernel.Sampler_create_sample(self) _IMP_base.UsageException: Usage check failure: No optimized particles found Context: MCCG Sampler 0::create_sample/MCCG Sampler 0::do_sample The code is pretty straightforward, sampler = IMP.core.MCCGSampler(m) sampler.set_bounding_box(bb) sampler.set_number_of_conjugate_gradient_steps(1000) sampler.set_number_of_monte_carlo_steps(1000) sampler.set_number_of_attempts(10) cs = sampler.create_sample What can I change to make this run again on 2.2? Thank you for your time, -- Joseph D. Eschweiler

2 1

IMP 2.2.0 release
by Ben Webb 10 Apr '14

10 Apr '14

IMP 2.2.0 is now available. It contains a number of new features, notably support for SOAP scoring and a more reliable RMF file format. See https://github.com/salilab/imp/releases/tag/2.2.0 for the full change log. Check it out at http://integrativemodeling.org/ As always, we'll make a a 2.2.1 release in a few weeks if any significant bugs show up in 2.2.0. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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RMF error while building
by Ibai Irastorza 07 Apr '14

07 Apr '14

Hi imp users, Yesterday I had 2 running imp's in 2 computers: 2.0.1 version and the developer version downloaded from github. I deleted both (imp folder and path lines from bash) to get the 2.1.1 version because I am still using IMP.restrainer and I need rmf module to make a movie. I get this error over and over again in both computers: [ 88%] /home/bioinfo/Programs/imp/swig/IMP_rmf.impl.i:1: Error: Unable to find 'RMF.i' Running swig on restrainer Traceback (most recent call last): File "/home/bioinfo/Programs/imp-2.0.1/tools/build/make_swig_wrapper.py", line 97, in <module> main() File "/home/bioinfo/Programs/imp-2.0.1/tools/build/make_swig_wrapper.py", line 90, in main run_swig(outputdir, options) File "/home/bioinfo/Programs/imp-2.0.1/tools/build/make_swig_wrapper.py", line 47, in run_swig % (ret, " ".join(args))) OSError: subprocess failed with return code 1: swig -castmode -interface _IMP_rmf -DPySwigIterator=IMP_RMF_PySwigIterator -DSwigPyIterator=IMP_RMF_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -I../../include -I../../swig -oh wrap.h-in -o wrap.cpp-in -I/home/bioinfo/Programs/imp/include -I/usr/include /home/bioinfo/Programs/imp/swig/IMP_rmf.i make[2]: *** [src/rmf_swig/wrap.cpp] Error 1 make[1]: *** [modules/rmf/pyext/CMakeFiles/_IMP_rmf.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... Linking CXX shared library ../../../lib/libimp_domino.so Scanning dependencies of target _IMP_restrainer [ 88%] Built target imp_domino [ 89%] Building CXX object modules/restrainer/pyext/CMakeFiles/_IMP_restrainer.dir/__/__/__/src/restrainer_swig/wrap.cpp.o Linking CXX shared module ../../../lib/_IMP_restrainer.so [ 89%] Built target _IMP_restrainer ^Cmake[2]: *** [modules/core/pyext/CMakeFiles/_IMP_core.dir/__/__/__/src/core_swig/wrap.cpp.o] Interrupt make[1]: *** [modules/core/pyext/CMakeFiles/_IMP_core.dir/all] Interrupt make[2]: *** [modules/atom/pyext/CMakeFiles/_IMP_atom.dir/__/__/__/src/atom_swig/wrap.cpp.o] Interrupt make[1]: *** [modules/atom/pyext/CMakeFiles/_IMP_atom.dir/all] Interrupt I searched for the RMF.i file it is ok located in rmf/dependency/RMF/swig/RMF.i I tried with all versions (even getting the RMF_source from git to get the module), I tried to turn off the network as Jan suggested here ,I tried the developer version also, installed the doxygen 1.8.5 version also and the same error always. I don't know what I am missing because yesterday I installed the 2.1.1 and the developer version in one of the computers without problems, and today does not work. I would really appreciate your help, 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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