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Re: [modeller_usage] loops and disulfide

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,....


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.


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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage