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[modeller_usage] mutation including fixed new-atom/old-atom distance



Dear modeller supporters,

I want to generate a single site mutation in a dimer and for this, I have successfully run mutate_model.py. However, in the new model, I would like to impose a fixed distance between a nitrogen from the mutated residue and an oxygen from a second residue that belongs to the other subunit. In detail:

I want to mutate residue 38 from molA to Arg, and impose that the NE from new Arg38 is at a 2.68 Angstroms distance of molB Glu27 OE1.

To impose this I understand I should write:

rsr.add(forms.gaussian(group=physical.xy_distance,

   feature=features.distance(at['OE1:27:B'],                          

                             at['NE:38:A']),

    mean=2.68, stdev=0.1))


But I don't know where to add this in mutate_model.py


Could you please help me with this?


With best regards,


Maria


--
Maria Solà
Dep. Structural Biology IBMB-CSIC
Barcelona Science Park (Helix Building)
Baldiri Reixac 15
08028 BARCELONA
Spain
Tel: (+34) 93 403 4950
Fax: (+34) 93 403 4979
e-mail: " target="_blank">