<div dir="ltr">You can use rmf_show and rmf_show -v to view your file in human readable format<div><a href="http://integrativemodeling.org/rmf/nightly/doc/executables.html">http://integrativemodeling.org/rmf/nightly/doc/executables.html</a> </div><div> </div><div>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.</div><div> </div><div>Barak</div></div> <div class="gmail_extra"> <div class="gmail_quote">On Thu, Jul 3, 2014 at 5:55 AM, Josh Bullock <<a href="mailto:jma.bullock@gmail.com" target="_blank">jma.bullock@gmail.com</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div dir="ltr">oh so there is something in the .rmf file, looks a bit garbled though ... is this normal ?<div> </div><div><a href="https://gist.github.com/mysticvision/271d973806603967fd31" target="_blank">https://gist.github.com/mysticvision/271d973806603967fd31</a> <div class="gmail_extra"> <div class="gmail_quote">On 3 July 2014 13:44, <<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" target="_blank">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" target="_blank">imp-users-request@salilab.org</a> You can reach the person managing the list at <a href="mailto:imp-users-owner@salilab.org" target="_blank">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" target="_blank">jma.bullock@gmail.com</a>> To: <a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">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" target="_blank">imp-users-request@salilab.org</a>> wrote: > Send IMP-users mailing list submissions to > <a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">imp-users-request@salilab.org</a> > > You can reach the person managing the list at > <a href="mailto:imp-users-owner@salilab.org" target="_blank">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" target="_blank">barak.raveh@gmail.com</a>> > To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">imp-users-request@salilab.org</a>> wrote: > > > >> Send IMP-users mailing list submissions to > >> <a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">imp-users-request@salilab.org</a> > >> > >> You can reach the person managing the list at > >> <a href="mailto:imp-users-owner@salilab.org" target="_blank">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" target="_blank">barak.raveh@gmail.com</a>> > >> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">imp-users-request@salilab.org</a>> wrote: > >> >> > >> >>> Send IMP-users mailing list submissions to > >> >>> <a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">imp-users-request@salilab.org</a> > >> >>> > >> >>> You can reach the person managing the list at > >> >>> <a href="mailto:imp-users-owner@salilab.org" target="_blank">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" target="_blank">barak.raveh@gmail.com</a>> > >> >>> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">imp-users-request@salilab.org</a>> wrote: > >> >>> > > >> >>> >> Send IMP-users mailing list submissions to > >> >>> >> <a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">imp-users-request@salilab.org</a> > >> >>> >> > >> >>> >> You can reach the person managing the list at > >> >>> >> <a href="mailto:imp-users-owner@salilab.org" target="_blank">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" target="_blank">barak.raveh@gmail.com</a>> > >> >>> >> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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 ***************************************** </blockquote></div> </div></div></div> _______________________________________________ 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> </blockquote></div> <div> </div>-- Barak </div>