how do you give/provide a secondary structure prediction to AbinitioRelax.linuxgccrelease? it is not obvious from online manual nor "-help" command option.
> 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.
> 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.
Thanks,
so it doesn't make much difference if I include the SS info to AbinitioRelax or not...
As you say, this is taken care of when building the fragment library then.