Joel Tyndall wrote: > I’m looking to generate a model with a disulfide constraint as well as > loop refinement. I am still getting my head around the python scripts. > In the old top files, one could do multiple things in the single top > file. I can’t seem to get past this issue with the python scripts. I can > run things separately but I am at a loss trying to combine them.
The Python scripts can do everything the TOP scripts did (plus a lot more, of course). Where in a TOP script you would redefine a function with a specific name (e.g. select_atoms) in Python you subclass automodel or loopmodel and override the method with the same name.
> I seem to be stuck with > > a = loopmodel(env,.... > > vs > > a = MyModel (having defined the disulfide patch
Just have MyModel subclass loopmodel rather than automodel (i.e. "class MyModel(loopmodel)") then you can use MyModel in exactly the same way as loopmodel, and get your disulfide patch at the same time as loop refinement.
> Could someone help or direct me to the write web page.
http://salilab.org/modeller/9v7/manual/node24.html
Just replace the class MyModel(automodel): line with class MyModel(loopmodel):
You can then set a.loop.starting_model etc. as in regular loop modeling.
> Is this the > process to actually run two separate cripts (generate disulfide then run > loop refinement?
No, the two can most certainly be combined.
Ben Webb, Modeller Caretaker