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make_fragments

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make_fragments
#1

We are trying to install make_fragments.pl locally still. Does anyone know about the neuralnet file that results from predict_2nd site? It seems to call overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net, but the predict_2nd package seems to have this:
t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-stride-seeded.net

Thanks,
Christy

Mon, 2009-09-21 12:42
ctaylor

> We are trying to install make_fragments.pl locally still. Does anyone know about the neuralnet file that results from predict_2nd site? It seems to call overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net, but the predict_2nd package seems to have this:
> t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-stride-seeded.net
>
> Thanks,
> Christy

Fri, 2009-09-25 10:15
AndrewBworth

I run make_fragments for CS-ROSETTA, and I've found, that, personally, I didn't need to run predict 2nd (I couldn't get it to compile properly, and I didn't really have the time to figure it out. ) Make_fragments works without all the secondary structure files.

Fri, 2009-09-25 10:17
AndrewBworth

Bump.

Christy, did you ever find this file? I sent you an email via the forums tool, but I'm not really sure it's working.

I seem to have basically followed Christy's steps in getting the make_fragments.pl tool, and I'm currently stuck on the missing overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net file used by predict-2nd. Has anyone actually put together a working make_fragments script?

Presumably Kevin Karplus has or knows how to generate this file, so I guess I'll ask him next.

Mon, 2011-02-07 13:21
bene

"Christy, did you ever find this file? I sent you an email via the forums tool, but I'm not really sure it's working."

Probably not - this thread was imported from the "old forums" but the user data was not transferred, so there's probably no recipient listed for that email.

(No, I don't know how to do the fragments, unfortunately...)

Mon, 2011-02-07 13:59
smlewis