dear Users,

I am sorry for the naif question, but is there a way to change the relative importance of restraints?

I am trying to add a secondary structure (both strand and sheet for H bonds) restraints to a model, in a region that do not align on the template structure (hence it shouldn't contain homology derived restraints). However only a few (up to 2) hydrogen bonds are formed rather than the whole beta sheet.

In case you wish to delve further into this I attach at the end the piece of code that I use to add the restraints:

Thank you very much for your help.

Regards,

Pietro

from modeller import * from modeller.automodel import * # Load the automodel class

# i tried also with automodel but there was no significant difference mdl = loopmodel(env, alnfile=already_done_alignment_filename, \ knowns = pdb_id, sequence = seq_id, \ loop_assess_methods=(assess.DOPE, assess.normalized_dope), \ assess_methods=(assess.DOPE, assess.normalized_dope) ) mdl.make_initial_model(aln) # Construct typical comparative modeling restraints mdl.mkhomcsr(selection(mdl), aln) mdl.restraints.add(secondary_structure.strand(mdl.residue_range('102:A', '108:A'))) # i know both of these regions are do align on anything (chain B is actually a 7 residues peptide I am adding, should be free to move anywhere). The residue numbering is read from initial model generated above mdl.restraints.add(secondary_structure.strand(mdl.residue_range('125:B:', '131:B'))) mdl.restraints.add(secondary_structure.sheet(mdl.atoms['N:102:A'], mdl.atoms['O:131:B'],sheet_h_bonds=-6)) mdl.restraints.make(selection(mdl), restraint_type='stereo', spline_on_site=False) mdl.restraints.condense() mdl.restraints.write(mdl.csrfile) # make the model env.edat.nonbonded_sel_atoms=1 # so that the selection interacts energetically with the unselected region. Actually I don't select anything manually, I added it just to be sure.. mdl.outputs = [] atmsel = mdl._check_select_atoms() mdl.multiple_models(atmsel) mdl.write_summary(mdl.outputs, 'models')