Dear all,
after some time, I updated IMP. Now the way I set up ConnectivityRestraints fails. I combine several particles to a pseudo-particle and the connectivity restraint gets a list of this pseudo-particles. The problem occurs in the moment, I try to evaluate the restraint. Attached is an example script, based on the connectivity example. That works still fine in an older IMP version, but now it gives me an error message "_IMP_base.InternalException: Not in input list. Violating object: "Model 0". Attribute x of particle "P3" with id 3" even though P3 has a x-value. What is wrong in my approach? Or what did change in the implementation? Is it related to the issue, that in my case particle.show() now only displays the name, but no attributes anymore? Furthermore, there is a "WARNING You should pass the model to the Restraint constructor. Constructing ConnectivityRestraint %1%", directly when I call IMP.core.ConnectivityRetraint. Is there a possibility to add the Model already at this point, which is not described in the documentation? I use set_model in the next line...
Thanks in advance!
Pia
Pia Unverdorben (Dipl. Math.) Max-Planck Institut für Biochemie Am Klopferspitz 18 D-82152 Martinsried
unverdor@biochem.mpg.de
I'll take a look. Thanks.
On Mon, Jul 1, 2013 at 2:44 AM, Pia Unverdorben unverdor@biochem.mpg.dewrote:
> Dear all, > > after some time, I updated IMP. Now the way I set up > ConnectivityRestraints fails. I combine several particles to a > pseudo-particle and the connectivity restraint gets a list of this > pseudo-particles. The problem occurs in the moment, I try to evaluate the > restraint. > Attached is an example script, based on the connectivity example. That > works still fine in an older IMP version, but now it gives me an error > message "_IMP_base.InternalException: Not in input list. Violating object: > "Model 0". Attribute x of particle "P3" with id 3" even though P3 has a > x-value. > What is wrong in my approach? Or what did change in the implementation? > Is it related to the issue, that in my case particle.show() now only > displays the name, but no attributes anymore? > Furthermore, there is a "WARNING You should pass the model to the > Restraint constructor. Constructing ConnectivityRestraint %1%", directly > when I call IMP.core.ConnectivityRetraint. Is there a possibility to add > the Model already at this point, which is not described in the > documentation? I use set_model in the next line... > > Thanks in advance! > > Pia > > > > > Pia Unverdorben (Dipl. Math.) > Max-Planck Institut für Biochemie > Am Klopferspitz 18 > D-82152 Martinsried > > unverdor@biochem.mpg.de > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >
There was a bug in LowestRefinedPairScore::get_inputs(). A fix will be pushed shortly. Pia, can I add you test to the misc module as a test? Thanks.
On Mon, Jul 1, 2013 at 9:46 AM, Daniel Russel drussel@gmail.com wrote:
> I'll take a look. Thanks. > > > On Mon, Jul 1, 2013 at 2:44 AM, Pia Unverdorben unverdor@biochem.mpg.dewrote: > >> Dear all, >> >> after some time, I updated IMP. Now the way I set up >> ConnectivityRestraints fails. I combine several particles to a >> pseudo-particle and the connectivity restraint gets a list of this >> pseudo-particles. The problem occurs in the moment, I try to evaluate the >> restraint. >> Attached is an example script, based on the connectivity example. That >> works still fine in an older IMP version, but now it gives me an error >> message "_IMP_base.InternalException: Not in input list. Violating object: >> "Model 0". Attribute x of particle "P3" with id 3" even though P3 has a >> x-value. >> What is wrong in my approach? Or what did change in the implementation? >> Is it related to the issue, that in my case particle.show() now only >> displays the name, but no attributes anymore? >> Furthermore, there is a "WARNING You should pass the model to the >> Restraint constructor. Constructing ConnectivityRestraint %1%", directly >> when I call IMP.core.ConnectivityRetraint. Is there a possibility to add >> the Model already at this point, which is not described in the >> documentation? I use set_model in the next line... >> >> Thanks in advance! >> >> Pia >> >> >> >> >> Pia Unverdorben (Dipl. Math.) >> Max-Planck Institut für Biochemie >> Am Klopferspitz 18 >> D-82152 Martinsried >> >> unverdor@biochem.mpg.de >> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> >
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Daniel Russel -
Pia Unverdorben