okay thanks for the advice.
Just trying to get SAXSRestraint working now ...
I get the following error:
> Profile is not sampled for q = 0.0054794, q_max = 0.5 > You can remove points with q > 0.5 from the experimental profile or > recompute the profile with higher max_q >
I'm slightly confused as 0.0054795 < 0.5, and also there are no values in my .dat file above 0.5. Finally, there doesn't seem to be a way to alter the max_q through the pmi module, would i have to go through the C++ ?
Thanks,
josh
try to use your experimental profile in the SAXSRestraint test, modules/pmi/test/test_saxs_restraint.py instead of "multi_A.pdb.dat" and see if you get the same error message from the test. you can also try foxs (with any protein and this profile) to see if your profile file format is ok.
On Wed, Nov 30, 2016 at 3:38 PM, Josh Bullock jma.bullock@gmail.com wrote:
> okay thanks for the advice. > > Just trying to get SAXSRestraint working now ... > > I get the following error: > >> Profile is not sampled for q = 0.0054794, q_max = 0.5 >> You can remove points with q > 0.5 from the experimental profile or >> recompute the profile with higher max_q >> > > I'm slightly confused as 0.0054795 < 0.5, and also there are no values in > my .dat file above 0.5. Finally, there doesn't seem to be a way to alter > the max_q through the pmi module, would i have to go through the C++ ? > > Thanks, > > josh > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >
foxs works fine.
test_saxs_restraint.py gives assertion errors:
> FAIL: test_SAXSRestraint (__main__.Tests) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "test_saxs_restraint.py", line 41, in test_SAXSRestraint > self.assertAlmostEqual(saxs_rest.evaluate(), 0.107, delta = 0.01) > AssertionError: 21.697142074172216 != 0.107 within 0.01 delta > > ====================================================================== > FAIL: test_SAXSRestraint_residue (__main__.Tests) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "test_saxs_restraint.py", line 51, in test_SAXSRestraint_residue > self.assertAlmostEqual(saxs_rest2.evaluate(), 0.491, delta = 0.01) > AssertionError: 21.832825619163884 != 0.491 within 0.01 delta > > ---------------------------------------------------------------------- > Ran 2 tests in 0.149s > > FAILED (failures=2) >
but i assume this is because the values being asserted apply to multi_A.pdb.dat.
i can send over the .dat file if that's helpful ?
thanks,
On 30 November 2016 at 14:44, Dina Schneidman duhovka@gmail.com wrote:
> try to use your experimental profile in the SAXSRestraint test, > modules/pmi/test/test_saxs_restraint.py instead of "multi_A.pdb.dat" and > see if you get the same error message from the test. > you can also try foxs (with any protein and this profile) to see if your > profile file format is ok. > > On Wed, Nov 30, 2016 at 3:38 PM, Josh Bullock jma.bullock@gmail.com > wrote: > >> okay thanks for the advice. >> >> Just trying to get SAXSRestraint working now ... >> >> I get the following error: >> >>> Profile is not sampled for q = 0.0054794, q_max = 0.5 >>> You can remove points with q > 0.5 from the experimental profile or >>> recompute the profile with higher max_q >>> >> >> I'm slightly confused as 0.0054795 < 0.5, and also there are no values in >> my .dat file above 0.5. Finally, there doesn't seem to be a way to alter >> the max_q through the pmi module, would i have to go through the C++ ? >> >> Thanks, >> >> josh >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >
it looks fine to me. I can look at your file, but the problem is probably not there. Can you try to minimize your code to a small unit test that fails?
On Wed, Nov 30, 2016 at 8:51 PM, Josh Bullock jma.bullock@gmail.com wrote:
> foxs works fine. > > test_saxs_restraint.py gives assertion errors: > > >> FAIL: test_SAXSRestraint (__main__.Tests) >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File "test_saxs_restraint.py", line 41, in test_SAXSRestraint >> self.assertAlmostEqual(saxs_rest.evaluate(), 0.107, delta = 0.01) >> AssertionError: 21.697142074172216 != 0.107 within 0.01 delta >> >> ====================================================================== >> FAIL: test_SAXSRestraint_residue (__main__.Tests) >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File "test_saxs_restraint.py", line 51, in test_SAXSRestraint_residue >> self.assertAlmostEqual(saxs_rest2.evaluate(), 0.491, delta = 0.01) >> AssertionError: 21.832825619163884 != 0.491 within 0.01 delta >> >> ---------------------------------------------------------------------- >> Ran 2 tests in 0.149s >> >> FAILED (failures=2) >> > > but i assume this is because the values being asserted apply to > multi_A.pdb.dat. > > i can send over the .dat file if that's helpful ? > > thanks, > > On 30 November 2016 at 14:44, Dina Schneidman duhovka@gmail.com wrote: > >> try to use your experimental profile in the SAXSRestraint test, >> modules/pmi/test/test_saxs_restraint.py instead of "multi_A.pdb.dat" and >> see if you get the same error message from the test. >> you can also try foxs (with any protein and this profile) to see if your >> profile file format is ok. >> >> On Wed, Nov 30, 2016 at 3:38 PM, Josh Bullock jma.bullock@gmail.com >> wrote: >> >>> okay thanks for the advice. >>> >>> Just trying to get SAXSRestraint working now ... >>> >>> I get the following error: >>> >>>> Profile is not sampled for q = 0.0054794, q_max = 0.5 >>>> You can remove points with q > 0.5 from the experimental profile or >>>> recompute the profile with higher max_q >>>> >>> >>> I'm slightly confused as 0.0054795 < 0.5, and also there are no values >>> in my .dat file above 0.5. Finally, there doesn't seem to be a way to alter >>> the max_q through the pmi module, would i have to go through the C++ ? >>> >>> Thanks, >>> >>> josh >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >>> >>> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >
sure. here is a minimal-ish version
> import IMP > import RMF > import IMP.atom > import IMP.rmf > import IMP.pmi > import IMP.pmi.topology > import IMP.pmi.dof > import IMP.pmi.macros > import IMP.pmi.restraints > import IMP.pmi.restraints.saxs > import IMP.pmi.restraints.basic > import IMP.pmi.representation > import IMP.pmi.tools > import IMP.pmi.samplers > import IMP.pmi.output > import IMP.pmi.macros > import IMP.pmi.topology
> seqs = IMP.pmi.topology.Sequences('data/seq.fasta') > > mdl = IMP.Model() > s = IMP.pmi.topology.System(mdl) > st = s.create_state() > > mols = [] > > prot = st.create_molecule("prot1",sequence=seqs["prot"],chain_id="A") > atomic = prot.add_structure(('data/prot.pdb'),chain_id=" ") > > prot.add_representation(atomic,resolutions=[1]) > > mols.append(prot) > > root_hier = s.build() > > dof = IMP.pmi.dof.DegreesOfFreedom(mdl) > for mol in mols: > dof.create_rigid_body(mol,nonrigid_parts=mol.get_non_atomic_residues()) > > ###################### RESTRAINTS ##################### > > output_objects = [] # keep a list of functions that need to be reported > rmf_restraints = [] > > ##SAXS setup > > saxs1 = IMP.pmi.restraints.saxs.SAXSRestraint(root_hier,"SAXS.dat") > saxs1.add_to_model() > output_objects.append(saxs1) > rmf_restraints.append(saxs1) > > ###################### SAMPLING ##################### > > rex=IMP.pmi.macros.ReplicaExchange0(mdl, > > root_hier=root_hier, > > crosslink_restraints=[], > > monte_carlo_sample_objects=dof.get_movers(), > > global_output_directory='multiscale_output/', > output_objects=output_objects, > monte_carlo_steps=10, > number_of_best_scoring_models=10, > > number_of_frames=50000) > rex.execute_macro() >
On 1 December 2016 at 15:56, Dina Schneidman duhovka@gmail.com wrote:
> it looks fine to me. I can look at your file, but the problem is probably > not there. > Can you try to minimize your code to a small unit test that fails? > > On Wed, Nov 30, 2016 at 8:51 PM, Josh Bullock jma.bullock@gmail.com > wrote: > >> foxs works fine. >> >> test_saxs_restraint.py gives assertion errors: >> >> >>> FAIL: test_SAXSRestraint (__main__.Tests) >>> ---------------------------------------------------------------------- >>> Traceback (most recent call last): >>> File "test_saxs_restraint.py", line 41, in test_SAXSRestraint >>> self.assertAlmostEqual(saxs_rest.evaluate(), 0.107, delta = 0.01) >>> AssertionError: 21.697142074172216 != 0.107 within 0.01 delta >>> >>> ====================================================================== >>> FAIL: test_SAXSRestraint_residue (__main__.Tests) >>> ---------------------------------------------------------------------- >>> Traceback (most recent call last): >>> File "test_saxs_restraint.py", line 51, in test_SAXSRestraint_residue >>> self.assertAlmostEqual(saxs_rest2.evaluate(), 0.491, delta = 0.01) >>> AssertionError: 21.832825619163884 != 0.491 within 0.01 delta >>> >>> ---------------------------------------------------------------------- >>> Ran 2 tests in 0.149s >>> >>> FAILED (failures=2) >>> >> >> but i assume this is because the values being asserted apply to >> multi_A.pdb.dat. >> >> i can send over the .dat file if that's helpful ? >> >> thanks, >> >> On 30 November 2016 at 14:44, Dina Schneidman duhovka@gmail.com wrote: >> >>> try to use your experimental profile in the SAXSRestraint test, >>> modules/pmi/test/test_saxs_restraint.py instead of "multi_A.pdb.dat" >>> and see if you get the same error message from the test. >>> you can also try foxs (with any protein and this profile) to see if your >>> profile file format is ok. >>> >>> On Wed, Nov 30, 2016 at 3:38 PM, Josh Bullock jma.bullock@gmail.com >>> wrote: >>> >>>> okay thanks for the advice. >>>> >>>> Just trying to get SAXSRestraint working now ... >>>> >>>> I get the following error: >>>> >>>>> Profile is not sampled for q = 0.0054794, q_max = 0.5 >>>>> You can remove points with q > 0.5 from the experimental profile or >>>>> recompute the profile with higher max_q >>>>> >>>> >>>> I'm slightly confused as 0.0054795 < 0.5, and also there are no values >>>> in my .dat file above 0.5. Finally, there doesn't seem to be a way to alter >>>> the max_q through the pmi module, would i have to go through the C++ ? >>>> >>>> Thanks, >>>> >>>> josh >>>> >>>> _______________________________________________ >>>> IMP-users mailing list >>>> IMP-users@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-users >>>> >>>> >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >>> >>> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >
-
Dina Schneidman -
Josh Bullock