Send IMP-users mailing list submissions to
    ">
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
    ">
You can reach the person managing the list at
    ">
When replying, please edit your Subject line so it is more specific
than "Re: Contents of IMP-users digest..."
Today's Topics:
 Â1. Re: Sampling and writing to pym/rmf (Josh Bullock) (Barak Raveh)
----------------------------------------------------------------------
Message: 1
Date: Thu, 3 Jul 2014 06:27:55 -0700
From: Barak Raveh <">>
To: Help and discussion for users of IMP <">>
Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Josh
    Bullock)
Message-ID:
    <">CAHp+>
Content-Type: text/plain; charset="utf-8"
You can use rmf_show and rmf_show -v to view your file in human readable
format
http://integrativemodeling.org/rmf/nightly/doc/executables.html
About chimera, are you using a latest nightly build? You can send me the
RMF file and I'll give a look to see if it depends on the chimera version.
Barak
On Thu, Jul 3, 2014 at 5:55 AM, Josh Bullock <">> wrote:
> oh so there is something in the .rmf file, looks a bit garbled though ...
> is this normal ?
>
> https://gist.github.com/mysticvision/271d973806603967fd31
>
>
> On 3 July 2014 13:44, <">> wrote:
>
>> Send IMP-users mailing list submissions to
>> Â Â Â Â ">
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
>> or, via email, send a message with subject or body 'help' to
>> Â Â Â Â ">
>>
>> You can reach the person managing the list at
>> Â Â Â Â ">
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of IMP-users digest..."
>>
>>
>> Today's Topics:
>>
>> Â Â1. 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 <">>
>> To: ">
>> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh)
>> Message-ID:
>> Â Â Â Â <CAHh_40_zsUCt4=
>> ">nZbvDRd0owHzz_v_DHEiB-R+>
>> 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()):
>> Â Â cs.load_configuration(i)
>> Â Â h = IMP.atom.Hierarchy.get_children(all)
>> Â Â tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
>> Â Â print "file is", tfn
>> Â Â rh = RMF.create_rmf_file(tfn)
>>
>> Â Â # add the hierarchy to the file
>> Â Â IMP.rmf.add_hierarchies(rh, h)
>>
>> Â Â # add the current configuration to the file as frame 0
>> Â Â IMP.rmf.save_frame(rh)
>>
>>
>> On 3 July 2014 00:20, <">> wrote:
>>
>> > Send IMP-users mailing list submissions to
>> > Â Â Â Â ">
>> >
>> > To subscribe or unsubscribe via the World Wide Web, visit
>> > Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
>> > or, via email, send a message with subject or body 'help' to
>> > Â Â Â Â ">
>> >
>> > You can reach the person managing the list at
>> > Â Â Â Â ">
>> >
>> > When replying, please edit your Subject line so it is more specific
>> > than "Re: Contents of IMP-users digest..."
>> >
>> >
>> > Today's Topics:
>> >
>> > Â Â1. Re: Sampling and writing to pym/rmf (Barak Raveh)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Wed, 2 Jul 2014 16:20:19 -0700
>> > From: Barak Raveh <">>
>> > To: Help and discussion for users of IMP <">>
>> > Subject: Re: [IMP-users] Sampling and writing to pym/rmf
>> > Message-ID:
>> > Â Â Â Â <
>> > ">CAHp+_Uoq-HAyca9AX_pFcEje32ke3J3KuKZWYfuj+>
>> > 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 <">>
>> > 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()):
>> > > Â Â cs.load_configuration(i)
>> > > Â Â h = IMP.atom.Hierarchy(m) Â Â# <------- how do i call the
>> hierarchy
>> > of
>> > > the current loaded configuration ?
>> > > Â Â c = p.get_children(h)
>> > > Â Â Âtfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
>> > > Â Â rh = RMF.create_rmf_file(tfn)
>> > >
>> > > Â Â # add the hierarchy to the file
>> > > Â Â IMP.rmf.add_hierarchies(rh, h)
>> > >
>> > > Â Â # add the current configuration to the file as frame 0
>> > > Â Â IMP.rmf.save_frame(rh)
>> > >
>> > > On 2 July 2014 23:03, <">> wrote:
>> > >
>> > >> Send IMP-users mailing list submissions to
>> > >> Â Â Â Â ">
>> > >>
>> > >> To subscribe or unsubscribe via the World Wide Web, visit
>> > >> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
>> > >> or, via email, send a message with subject or body 'help' to
>> > >> Â Â Â Â ">
>> > >>
>> > >> You can reach the person managing the list at
>> > >> Â Â Â Â ">
>> > >>
>> > >> When replying, please edit your Subject line so it is more specific
>> > >> than "Re: Contents of IMP-users digest..."
>> > >>
>> > >>
>> > >> Today's Topics:
>> > >>
>> > >> Â Â1. Re: Sampling and writing to pym/rmf (Barak Raveh)
>> > >>
>> > >>
>> > >>
>> ----------------------------------------------------------------------
>> > >>
>> > >> Message: 1
>> > >> Date: Wed, 2 Jul 2014 15:03:19 -0700
>> > >>
>> > >> From: Barak Raveh <">>
>> > >> To: Help and discussion for users of IMP <">>
>> > >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf
>> > >> Message-ID:
>> > >> Â Â Â Â <CAHp+_UqO8rXRMsUSndbg-c0jyDxnswDe9aFKvW889gGMU=
>> > >> ">>
>> > >> 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 <">>
>> > >> 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 <
>> ">>
>> > >> > wrote:
>> > >> >
>> > >> >> ah sorry ! this line gives me the error
>> > >> >>
>> > >> >> h= IMP.atom.Hierarchy.get_children(cs)
>> > >> >>
>> > >> >> thanks
>> > >> >>
>> > >> >> josh
>> > >> >>
>> > >> >> On 2 July 2014 17:45, <">> wrote:
>> > >> >>
>> > >> >>> Send IMP-users mailing list submissions to
>> > >> >>> Â Â Â Â ">
>> > >> >>>
>> > >> >>> To subscribe or unsubscribe via the World Wide Web, visit
>> > >> >>> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
>> > >> >>> or, via email, send a message with subject or body 'help' to
>> > >> >>> Â Â Â Â ">
>> > >> >>>
>> > >> >>> You can reach the person managing the list at
>> > >> >>> Â Â Â Â ">
>> > >> >>>
>> > >> >>> When replying, please edit your Subject line so it is more
>> specific
>> > >> >>> than "Re: Contents of IMP-users digest..."
>> > >> >>>
>> > >> >>>
>> > >> >>> Today's Topics:
>> > >> >>>
>> > >> >>> Â Â1. 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 <">>
>> > >> >>> To: Help and discussion for users of IMP <">>
>> > >> >>> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak
>> > Raveh)
>> > >> >>> Message-ID:
>> > >> >>> Â Â Â Â <CAHp+_Uo19VasJDJYi+2CoUUu=
>> > >> >>> ">u_6duKCraVetU4dW45+>
>> > >> >>> Content-Type: text/plain; charset="utf-8"
>> > >> >>>
>> > >> >>> Which lines throws the error?
>> > >> >>>
>> > >> >>>
>> > >> >>> On Wed, Jul 2, 2014 at 4:56 AM, Josh Bullock <
>> ">
>> > >
>> > >> >>> 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()):
>> > >> >>> > Â Â JOSH = cs.load_configuration(i)
>> > >> >>> > Â Â S= IMP.atom.Selection
>> > >> >>> > Â Â h= IMP.atom.Hierarchy.get_children(cs)
>> > >> >>> > Â Â tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
>> > >> >>> > Â Â rh = RMF.create_rmf_file(tfn)
>> > >> >>> >
>> > >> >>> > On 1 July 2014 17:31, <">> wrote:
>> > >> >>> >
>> > >> >>> >> Send IMP-users mailing list submissions to
>> > >> >>> >> Â Â Â Â ">
>> > >> >>> >>
>> > >> >>> >> To subscribe or unsubscribe via the World Wide Web, visit
>> > >> >>> >> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
>> > >> >>> >> or, via email, send a message with subject or body 'help' to
>> > >> >>> >> Â Â Â Â ">
>> > >> >>> >>
>> > >> >>> >> You can reach the person managing the list at
>> > >> >>> >> Â Â Â Â ">
>> > >> >>> >>
>> > >> >>> >> When replying, please edit your Subject line so it is more
>> > specific
>> > >> >>> >> than "Re: Contents of IMP-users digest..."
>> > >> >>> >>
>> > >> >>> >>
>> > >> >>> >> Today's Topics:
>> > >> >>> >>
>> > >> >>> >> Â Â1. Re: Sampling and writing to pym/rmf (Barak Raveh)
>> > >> >>> >>
>> > >> >>> >>
>> > >> >>> >>
>> > >>
>> ----------------------------------------------------------------------
>> > >> >>> >>
>> > >> >>> >> Message: 1
>> > >> >>> >> Date: Tue, 1 Jul 2014 09:31:33 -0700
>> > >> >>> >> From: Barak Raveh <">>
>> > >> >>> >> To: Help and discussion for users of IMP <
>> ">>
>> > >> >>> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf
>> > >> >>> >> Message-ID:
>> > >> >>> >> Â Â Â Â <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ=
>> > >> >>> >> ">>
>> > >> >>> >> 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 <
>> > >> ">>
>> > >> >>> >> 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),
>> > >> >>> >> > Â Â Â Â Â Â Â Â Â Â Â Â Â Â ÂIMP.algebra.Vector3D(300, 300,
>> > 300))
>> > >> >>> >> >
>> > >> >>> >> >
>> > >> >>> >> > # this function creates the molecular hierarchies for the
>> > various
>> > >> >>> >> involved
>> > >> >>> >> > proteins
>> > >> >>> >> > def create_representation():
>> > >> >>> >> > Â Â m= IMP.Model()
>> > >> >>> >> > Â Â all=IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
>> > >> >>> >> > Â Â all.set_name("the universe")
>> > >> >>> >> > Â Â # create a protein, represented as a set of connected
>> balls
>> > >> of
>> > >> >>> >> > appropriate
>> > >> >>> >> > Â Â # radii and number, chose by the resolution parameter
>> and
>> > the
>> > >> >>> >> number of
>> > >> >>> >> > Â Â # amino acids.
>> > >> >>> >> >
>> > >> >>> >> > Â Â def create_protein_from_pdbs(name, files):
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â def create_from_pdb(file):
>> > >> >>> >> > Â Â Â Â Â Â sls=IMP.SetLogState(IMP.NONE)
>> > >> >>> >> > Â Â Â Â Â Â datadir = os.getcwd()
>> > >> >>> >> > Â Â Â Â Â Â print datadir
>> > >> >>> >> > Â Â t=IMP.atom.read_pdb( datadir+'/' + file, m,
>> > >> >>> >> > Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ÂIMP.atom.ATOMPDBSelector())
>> > >> >>> >> > Â Â Â Â Â Â del sls
>> > >> >>> >> > Â Â Â Â Â Â #IMP.atom.show_molecular_hierarchy(t)
>> > >> >>> >> > Â Â Â Â Â Â c=IMP.atom.Chain(IMP.atom.get_by_type(t,
>> > >> >>> >> > IMP.atom.CHAIN_TYPE)[0])
>> > >> >>> >> > Â Â Â Â Â Â if c.get_number_of_children()==0:
>> > >> >>> >> > Â Â Â Â Â Â Â Â IMP.atom.show_molecular_hierarchy(t)
>> > >> >>> >> > Â Â Â Â Â Â # there is no reason to use all atoms, just
>> > >> approximate
>> > >> >>> the
>> > >> >>> >> > pdb shape instead
>> > >> >>> >> > Â Â Â Â Â Â s=IMP.atom.create_simplified_along_backbone(c,
>> > >> >>> >> >
>> > >> >>> >> resolution/300.0)
>> > >> >>> >> > Â Â Â Â Â Â IMP.atom.destroy(t)
>> > >> >>> >> > Â Â Â Â Â Â # make the simplified structure rigid
>> > >> >>> >> > Â Â Â Â Â Â rb=IMP.atom.create_rigid_body(s)
>> > >> >>> >> > # Â Â Â Â Â Ârb=IMP.atom.create_rigid_body(c)
>> > >> >>> >> > Â Â Â Â Â Â rb.set_coordinates_are_optimized(True)
>> > >> >>> >> > Â Â Â Â Â Â return s
>> > >> >>> >> > # Â Â Â Â Â Âreturn c
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â h= create_from_pdb(files[0])
>> > >> >>> >> > Â Â Â Â h.set_name(name)
>> > >> >>> >> > Â Â Â Â all.add_child(h)
>> > >> >>> >> >
>> > >> >>> >> > Â Â create_protein_from_pdbs("A", [Firstpdb])
>> > >> >>> >> > Â Â create_protein_from_pdbs("B", [Secondpdb])
>> > >> >>> >> > Â Â create_protein_from_pdbs("C", [Thirdpdb])
>> > >> >>> >> > Â Â create_protein_from_pdbs("D", [Fourthpdb])
>> > >> >>> >> > Â Â #create_protein_from_pdbs("C", ["rpt3_imp.pdb"])
>> > >> >>> >> > Â Â return (m, all)
>> > >> >>> >> >
>> > >> >>> >> > # create the needed restraints and add them to the model
>> > >> >>> >> >
>> > >> >>> >> > def create_restraints(m, all):
>> > >> >>> >> > Â Â def add_connectivity_restraint(s):
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â tr= IMP.core.TableRefiner()
>> > >> >>> >> > Â Â Â Â rps=[]
>> > >> >>> >> > Â Â Â Â for sc in s:
>> > >> >>> >> > Â Â Â Â Â Â ps= sc.get_selected_particles()
>> > >> >>> >> > Â Â Â Â Â Â rps.append(ps[0])
>> > >> >>> >> > Â Â Â Â Â Â tr.add_particle(ps[0], ps)
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â # duplicate the
>> IMP.atom.create_connectivity_restraint
>> > >> >>> >> > functionality
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â score=
>> > >> >>> >> >
>> > >> >>> >>
>> > >> >>>
>> > >>
>> >
>> IMP.core.KClosePairsPairScore(IMP.core.HarmonicSphereDistancePairScore(0,1),tr)
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â r= IMP.core.MSConnectivityRestraint(m,score)
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â iA = r.add_type([rps[0]])
>> > >> >>> >> > Â Â Â Â iB = r.add_type([rps[1]])
>> > >> >>> >> > Â Â Â Â iC = r.add_type([rps[2]])
>> > >> >>> >> > Â Â Â Â iD = r.add_type([rps[3]])
>> > >> >>> >> > Â Â Â Â n1 = r.add_composite([iA, iB, iC, iD])
>> > >> >>> >> > Â Â Â Â n2 = r.add_composite([iA, iB], n1)
>> > >> >>> >> > Â Â Â Â n3 = r.add_composite([iC, iD], n1)
>> > >> >>> >> > Â Â Â Â n4 = r.add_composite([iB, iC, iD], n1)
>> > >> >>> >> >
>> > >> >>> >> > Â Â Â Â m.add_restraint(r)
>> > >> >>> >> >
>> > >> >>> >> > Â Â evr=IMP.atom.create_excluded_volume_restraint([all])
>> > >> >>> >> > Â Â m.add_restraint(evr)
>> > >> >>> >> > Â Â # a Selection allows for natural specification of what
>> the
>> > >> >>> >> restraints
>> > >> >>> >> > act on
>> > >> >>> >> > Â Â S= IMP.atom.Selection
>> > >> >>> >> > Â Â sA=S(hierarchy=all, molecule="A")
>> > >> >>> >> > Â Â sB=S(hierarchy=all, molecule="B")
>> > >> >>> >> > Â Â sC=S(hierarchy=all, molecule="C")
>> > >> >>> >> > Â Â sD=S(hierarchy=all, molecule="D")
>> > >> >>> >> > Â Â add_connectivity_restraint([sA, sB, sC, sD])
>> > >> >>> >> >
>> > >> >>> >> >
>> > >> >>> >> > # find acceptable conformations of the model
>> > >> >>> >> > def get_conformations(m):
>> > >> >>> >> > Â Â sampler= IMP.core.MCCGSampler(m)
>> > >> >>> >> > Â Â sampler.set_bounding_box(bb)
>> > >> >>> >> > Â Â # magic numbers, experiment with them and make them
>> large
>> > >> >>> enough for
>> > >> >>> >> > things to work
>> > >> >>> >> > Â Â sampler.set_number_of_conjugate_gradient_steps(100)
>> > >> >>> >> > Â Â sampler.set_number_of_monte_carlo_steps(20)
>> > >> >>> >> > Â Â sampler.set_number_of_attempts(models)
>> > >> >>> >> > Â Â # We don't care to see the output from the sampler
>> > >> >>> >> > Â Â sampler.set_log_level(IMP.SILENT)
>> > >> >>> >> > Â Â # return the IMP.ConfigurationSet storing all the found
>> > >> >>> >> configurations
>> > >> >>> >> > that
>> > >> >>> >> > Â Â # meet the various restraint maximum scores.
>> > >> >>> >> > Â Â cs= sampler.create_sample()
>> > >> >>> >> > Â Â return cs
>> > >> >>> >> >
>> > >> >>> >> >
>> > >> >>> >> > # cluster the conformations and write them to a file
>> > >> >>> >> > def analyze_conformations(cs, all, gs):
>> > >> >>> >> > Â Â # we want to cluster the configurations to make them
>> easier
>> > >> to
>> > >> >>> >> > understand
>> > >> >>> >> > Â Â # in the case, the clustering is pretty meaningless
>> > >> >>> >> > Â Â embed= IMP.statistics.ConfigurationSetXYZEmbedding(cs,
>> > >> >>> >> >
>> > >> >>> >> >
>> > ÂIMP.container.ListSingletonContainer(IMP.atom.get_leaves(all)),
>> > >> >>> True)
>> > >> >>> >> > Â Â cluster= IMP.statistics.create_lloyds_kmeans(embed, 10,
>> > >> 10000)
>> > >> >>> >> > Â Â # dump each cluster center to a file so it can be
>> viewed.
>> > >> >>> >> > Â Â for i in range(cluster.get_number_of_clusters()):
>> > >> >>> >> > Â Â Â Â center= cluster.get_cluster_center(i)
>> > >> >>> >> > Â Â Â Â cs.load_configuration(i)
>> > >> >>> >> > Â Â Â Â w= IMP.display.PymolWriter("cluster.%d.pym"%i)
>> > >> >>> >> > Â Â Â Â for g in gs:
>> > >> >>> >> > Â Â Â Â Â Â 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()):
>> > >> >>> >> > Â Â color= IMP.display.get_display_color(i)
>> > >> >>> >> > Â Â n= all.get_child(i)
>> > >> >>> >> > Â Â name= n.get_name()
>> > >> >>> >> > Â Â g= IMP.atom.HierarchyGeometry(n)
>> > >> >>> >> > Â Â g.set_color(color)
>> > >> >>> >> > Â Â 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()):
>> > >> >>> >> > Â Â Â Â cs.load_configuration(i)
>> > >> >>> >> > Â Â Â Â # print the configuration
>> > >> >>> >> > Â Â Â Â print "solution number: ",i,"scored :",
>> > m.evaluate(False)
>> > >> >>> >> > Â Â Â Â 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()):
>> > >> >>> >> > Â Â JOSH = cs.load_configuration(i)
>> > >> >>> >> > Â Â S= IMP.atom.Selection
>> > >> >>> >> > Â Â h= IMP.atom.Hierarchy.get_children(cs)
>> > >> >>> >> > Â Â tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
>> > >> >>> >> > Â Â rh = RMF.create_rmf_file(tfn)
>> > >> >>> >> >
>> > >> >>> >> > Â Â # add the hierarchy to the file
>> > >> >>> >> > Â Â IMP.rmf.add_hierarchies(rh, h)
>> > >> >>> >> >
>> > >> >>> >> > Â Â # add the current configuration to the file as frame 0
>> > >> >>> >> > Â Â IMP.rmf.save_frame(rh)
>> > >> >>> >> >
>> > >> >>> >> > Â Â for g in gs:
>> > >> >>> >> > Â Â Â Â w.add_geometry(g)
>> > >> >>> >> >
>> > >> >>> >> > analyze_conformations(cs, all, gs)
>> > >> >>> >> >
>> > >> >>> >> >
>> > >> >>> >> > _______________________________________________
>> > >> >>> >> > IMP-users mailing list
>> > >> >>> >> > ">
>> > >> >>> >> > https://salilab.org/mailman/listinfo/imp-users
>> > >> >>> >> >
>> > >> >>> >> >
>> > >> >>> >>
>> > >> >>> >>
>> > >> >>> >> --
>> > >> >>> >> Barak
>> > >> >>> >> -------------- next part --------------
>> > >> >>> >> An HTML attachment was scrubbed...
>> > >> >>> >> URL: <
>> > >> >>> >>
>> > >> >>>
>> > >>
>> >
>> http://salilab.org/archives/imp-users/attachments/20140701/7b0e5f9f/attachment.html
>> > >> >>> >> >
>> > >> >>> >>
>> > >> >>> >> ------------------------------
>> > >> >>>
>> > >> >>> >>
>> > >> >>> >> _______________________________________________
>> > >> >>> >> IMP-users mailing list
>> > >> >>> >> ">
>> > >> >>> >> https://salilab.org/mailman/listinfo/imp-users
>> > >> >>> >>
>> > >> >>> >>
>> > >> >>> >> End of IMP-users Digest, Vol 38, Issue 2
>> > >> >>> >> ****************************************
>> > >> >>>
>> > >> >>> >>
>> > >> >>> >
>> > >> >>> >
>> > >> >>> > _______________________________________________
>> > >> >>> > IMP-users mailing list
>> > >> >>> > ">
>> > >> >>> > https://salilab.org/mailman/listinfo/imp-users
>> > >> >>> >
>> > >> >>> >
>> > >> >>>
>> > >> >>>
>> > >> >>> --
>> > >> >>> Barak
>> > >> >>> -------------- next part --------------
>> > >> >>> An HTML attachment was scrubbed...
>> > >> >>> URL: <
>> > >> >>>
>> > >>
>> >
>> http://salilab.org/archives/imp-users/attachments/20140702/081e70ca/attachment.html
>> > >> >>> >
>> > >> >>>
>> > >> >>> ------------------------------
>> > >> >>>
>> > >> >>>
>> > >> >>> _______________________________________________
>> > >> >>> IMP-users mailing list
>> > >> >>> ">
>> > >> >>> https://salilab.org/mailman/listinfo/imp-users
>> > >> >>>
>> > >> >>>
>> > >> >>> End of IMP-users Digest, Vol 38, Issue 4
>> > >> >>> ****************************************
>> > >> >>>
>> > >> >>
>> > >> >>
>> > >> >> _______________________________________________
>> > >> >> IMP-users mailing list
>> > >> >> ">
>> > >> >> https://salilab.org/mailman/listinfo/imp-users
>> > >> >>
>> > >> >>
>> > >> >
>> > >> >
>> > >> > --
>> > >> > Barak
>> > >> >
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> Barak
>> > >> -------------- next part --------------
>> > >> An HTML attachment was scrubbed...
>> > >> URL: <
>> > >>
>> >
>> http://salilab.org/archives/imp-users/attachments/20140702/74f552a1/attachment.html
>> > >> >
>> > >>
>> > >>
>> > >> ------------------------------
>> > >>
>> > >> _______________________________________________
>> > >> IMP-users mailing list
>> > >> ">
>> > >> https://salilab.org/mailman/listinfo/imp-users
>> > >>
>> > >>
>> > >> End of IMP-users Digest, Vol 38, Issue 7
>> > >> ****************************************
>> > >>
>> > >
>> > >
>> > > _______________________________________________
>> > > IMP-users mailing list
>> > > ">
>> > > https://salilab.org/mailman/listinfo/imp-users
>> > >
>> > >
>> >
>> >
>> > --
>> > Barak
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> > URL: <
>> >
>> http://salilab.org/archives/imp-users/attachments/20140702/2f1fb30c/attachment.html
>> > >
>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > IMP-users mailing list
>> > ">
>> > https://salilab.org/mailman/listinfo/imp-users
>> >
>> >
>> > End of IMP-users Digest, Vol 38, Issue 9
>> > ****************************************
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://salilab.org/archives/imp-users/attachments/20140703/fe3a183b/attachment.html
>> >
>>
>> ------------------------------
>>
>> _______________________________________________
>> IMP-users mailing list
>> ">
>> https://salilab.org/mailman/listinfo/imp-users
>>
>>
>> End of IMP-users Digest, Vol 38, Issue 10
>> *****************************************
>>
>
>
> _______________________________________________
> IMP-users mailing list
> ">
> https://salilab.org/mailman/listinfo/imp-users
>
>
--
Barak
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://salilab.org/archives/imp-users/attachments/20140703/ebc4da96/attachment.html>
------------------------------
_______________________________________________
IMP-users mailing list
">
https://salilab.org/mailman/listinfo/imp-users
End of IMP-users Digest, Vol 38, Issue 12
*****************************************