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 list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users