> Hi,
>
> how do you give/provide a secondary structure prediction to AbinitioRelax.linuxgccrelease? it is not obvious from online manual nor “-help” command option.
>
> Thanks!
This command line flag is used to provide a prediction during AbinitioRelax, but its only used for some of the filters.
-in::file::psipred_ss2 psipred_ss2 file
The secondary structure prediction is primarily used to generate the fragments, and the fragments themselves are responsible for enforcing that prediction.
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