On 2/1/12 2:27 PM, Stephanie Schaefer wrote: > I am new to modeler, but what I have done is edited the template PDB > (wildtype) to remove the active site disulfide (SSbond) and then > generated a homology model using the modified wt PDB as the template. > Is this the correct approach to generating a reduced active site > model?
Modeller doesn't use the SSBOND entries in the PDB file - it looks at the geometry instead: http://salilab.org/modeller/9.10/manual/node179.html
So modifying the SSBOND entries won't remove the disulfide bridges. Disulfide bridges are added automatically during homology modeling. If you really want to turn off this behavior, you can override the automodel.default_patches() method (which normally calls patch_ss_templates, above) with a script like the following:
from modeller import * from modeller.automodel import *
class MyModel(automodel): def default_patches(self, aln): # do nothing, not even disulfide patching pass
then continue as normal but use the MyModel class rather than automodel in your script (e.g. a = MyModel(env, alnfile=..., knowns=..., sequence=...)).
I should warn you however that Modeller builds models that structurally resemble the template (this is by construction - it's how template-based modeling works). So your model is likely to have a similar backbone to the template, and even though you're not forcing the disulfide bonds, the two cysteines will probably still end up being close.
Ben Webb, Modeller Caretaker