Re: [modeller_usage] Is there anything wrong with my configuration file?My models look so strange

[Modeller Caretaker <modeller-care@ucsf.edu>]

wayj86 wayj86 wrote:
> Two days ago I wanted to model an antibody with specifying the CDR
> regions.Here is my configuation file:
...
> I don't know what is wrong with it but the models it built were so
> strange,I can see some breakpoints in the structures.

Your script is a little optimistic - you are asking Modeller to
simultaneously optimize 6 loops, some of which are themselves over the
sampling limit (12 residues) yet you are building only two loop models
for each model, which is nowhere near enough sampling. (For a 12-residue
loop, we typically recommend 500 loop models or more for adequate
sampling.) In your case, you would probably want to optimize each loop
individually, and then combine the best models for each loop.

	Ben Webb, Modeller Caretaker
-- 
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