input secondary structure prediction to AbinitioRelax

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input secondary structure prediction to AbinitioRelax
#1

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!

Mon, 2010-08-09 12:36
biofisikx

> 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.

Tue, 2010-08-10 12:19
robert.vernon

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.

Wed, 2010-08-11 08:01
biofisikx