Thank you very much for your answer!
On 24 July 2013 19:59, Jan Kosinski kosinski@embl.de wrote:
> Hi, > > If you look to the do_global_fitting code you will see that basically it > runs do_local_fitting with max_trans calculated based on the size of the > box around EM map: > FFTFittingOutput *FFTFitting::do_global_fitting(em::DensityMap *dmap, > double density_threshold, > atom::Hierarchy mol2fit, > double angle_sampling_interval_rad, > int num_fits_to_report, > double max_clustering_translation, > double max_clustering_angle, > bool cluster_fits, > int num_angle_per_voxel, > const std::string &angles_filename){ > algebra::BoundingBox3D bb = em::get_bounding_box(dmap); > algebra::Vector3D b1,b2; > b1=bb.get_corner(0); > b2=bb.get_corner(1); > double max_trans=std::max(1.2*(b2[0]-b1[0]), > 1.2*(b2[1]-b1[1])); > max_trans=std::max(max_trans, > 1.2*(b2[2]-b2[2])); > return do_local_fitting(dmap, density_threshold, > mol2fit, > angle_sampling_interval_rad, > IMP::PI, max_trans, num_fits_to_report, > cluster_fits, > num_angle_per_voxel, > max_clustering_translation, max_clustering_angle, > angles_filename); > > So, if your PDB structure is close enough the map, it may reach the map > within max_trans distance at some point, and the fit will work. If it is > too far away, it will fail. I think it could be considered as a bug, > especially that if may affect the whole MultiFit application (I was able to > get 'No fits found' by fit_fft step of MulitFit by moving a protein far > away from the map). > > For the time being, just move your protein to the center of the map. I am > not sure if it makes sense to report the problem, MultiFit doesn't seem to > be currently being developed, at least not in the official imp github repo > ( https://github.com/salilab/imp/tree/develop/modules/multifit). > > I hope it helps, > Jan > > > On 07/15/2013 09:26 AM, Dan Cohen wrote: > > Hello, > > I have been using do_global_fitting function to fit a PDB into an EM map. > I'm getting tons of warnings in the stdout such as : > > WARNING particle:Atom C of residue 52 is not interpolated > WARNING particle:Atom O of residue 52 is not interpolated > WARNING particle:Atom N of residue 53 is not interpolated > WARNING particle:Atom C of residue 40 is not interpolated > WARNING particle:Atom O of residue 40 is not interpolated > WARNING particle:Atom N of residue 41 is not interpolated > WARNING particle:Atom CA of residue 41 is not interpolated > > According to my understanding this means that the PDB is located outside > the > bounding box of the EM-file - is that true? > > Hows does the algorithm decide with which respective translations to test > the fitting? > > Why doesn't the algorithm just move the the protein's center of mass to > the center of the EM > file, before starting the processing? Should I do that manually? > > Thank you, > Dany > > > > _______________________________________________ > IMP-users mailing listIMP-users@salilab.orghttps://salilab.org/mailman/listinfo/imp-users > > > > -- > Jan Kosinski, PhD > Structural and Computational Biology Unit > European Molecular Biology Laboratory (EMBL) > Meyerhofstrasse 1 > 69117 Heidelberg > Germany > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >