Entering edit mode
12.5 years ago
Harpalss
▴
310
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?
Superimposed?
I think both 'superposed" and 'superimposed' is correct...
You'd better ask at modeller_usage mailing list: http://salilab.org/mailman/listinfo/modeller_usage .