Re: [modeller_usage] How to use model.patch_ss_templates() ?

[Modeller Caretaker <>]

jitrayut jitonnom wrote:
> I am new for this program and i doubt on how to use 
> model.patch_ss_templates() in order to model disulfide bond of our model 
> from templates. As i read the FAQ no. 3, i am stil not understand that
> where *_patch_disulfides.py_* be used. Since I know  from the advanced 
> tutorials that there are many steps to run multiple template such as 
> salign.py , align2d_mult.py, model_mult.py, and evaluate_model.py. So, 
> which steps should be insertedt the patch_disulfides.py ?  

salign.py and align2d_mult.py are for alignment, and evaluate_model.py 
is for model evaluation. In all of these cases the definition of 
disulfide bonds is not required. model.patch_ss_templates() adds 
disulfide bonds in the model, if it is aligned with a template which has 
a disulfide. This is called automatically for you for 'automodel' so you 
don't generally need to worry about it.

An example is given in FAQ #3 of how to add specific disulfide bonds in 
the 'automodel' procedure, using model.patch(). This only applies to the 
model building step, of course - model_mult.py in your case.

	Ben Webb, Modeller Caretaker
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