Calculate Distance Between Two Superposed Equivalent Atoms

Question

[Harpalss]

So I can superpose two structures with modeller using the following code:

    def get_rmsd(self, template, model_strucutre):

    from modeller import *

    # Create the environment and append alignment for template
    env = environ()
    aln = alignment(env)
    mdl = model(env, file='./modeller/templates/'+template)
    aln.append_model(mdl, align_codes='Temptlate = %s' % template[-8:], atom_files='Template')

    # Create model environment and append to alignment
    mdl2 = model(env, file='./modeller/models/'+model_strucutre)
    aln.append_model(mdl2, align_codes='model = %s' % model_strucutre, atom_files='Model')
    aln.align(gap_penalties_1d=(-600, -400))
    aln.write(file=model_strucutre[:-4]+'.ali')
    atmsel = selection(mdl).only_atom_types('CA')
    r = atmsel.superpose(mdl2, aln)
    rms = r.rms
    drms = r.drms
    aln.clear()

When it calculates the RMSD is must know the distance between two equivalent C-alpha atoms. Is there away of extracting the distance between two equivalent C-alpha atoms?

[Egon Willighagen]

Superimposed?

[Jan Kosinski]

I think both 'superposed" and 'superimposed' is correct...

[Jan Kosinski]

You'd better ask at modeller_usage mailing list: http://salilab.org/mailman/listinfo/modeller_usage .

Answer 1

[João Rodrigues]

I don't know if they are actually stored somewhere, but you can retrieve them by iterating over the atoms and calculating from the coordinates manually. Check here or here.