Ben - from the warning messages I see that you are using the FitRestraint. Are you using any other restraints as well? It will be useful to get your optimization script so we can take a look. Keren. On Aug 12, 2010, at 7:00 AM, Benjamin SCHWARZ wrote:
> As evoked in a former message, I couldn't manage to have GC > optimizer working with the binary MAC OSX version (IMP 1.0). So I > compiled the latest version on one of our linux machines. The > compilation was easily achieved with the default parameters, though > I guess it could be possible to enhance IMP speed by tweaking some > magic compilation parameters… I'll see this point later. > > I am thus using IMP version SVN 6211 > > With this version CG optimizer seem to work fine, though I always > get warning messages > WARNING could not find parameters for radius:1.85 > WARNING Setting params for radius :1.85 > WARNING could not find parameters for radius:2.275 > WARNING Setting params for radius :2.275 > WARNING could not find parameters for radius:2 > WARNING Setting params for radius :2 > WARNING could not find parameters for radius:1.7 > WARNING Setting params for radius :1.7 > WARNING could not find parameters for radius:2.175 > WARNING Setting params for radius :2.175 > WARNING could not find parameters for radius:2.06 > WARNING Setting params for radius :2.06 > WARNING could not find parameters for radius:1.77 > WARNING Setting params for radius :1.77 > WARNING could not find parameters for radius:1.9924 > WARNING Setting params for radius :1.9924 > WARNING could not find parameters for radius:1.8 > WARNING Setting params for radius :1.8 > WARNING Object "Nameless" was never used. See the > IMP::Object documentation for an explanation. > > > But when trying to use CG in conjunction with MC > ( mco.set_local_optimizer( cgo ) ), I still experience problems; > sometimes it seems to pole in an infinite loop, sometimes it > prematurely ends with this message : > > Traceback (most recent call last): > File "./fitWithRestraints.py", line 222, in <module> > opti.optimize(params["optimizer"]["maxSteps"]) > File "/usr/local/imp/lib64/python2.6/site-packages/IMP/ > __init__.py", line 1569, in optimize > def optimize(self, *args): return _IMP.Optimizer_optimize(self, > *args) > _IMP.UsageException: Attempt to use uninitialized vector. > > > Ultimately, I am wondering if trying to get CG working is not a > waste of time for me… I mean, maybe there are better approaches... > So, If you have any comment or general advice that I should check, > feel free to do so. > > --Ben > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users