Reply To: protein structure prediction using relax — high-powered jobs

[Anonymous]

My alignment file is in this format.
## FJ637 2h1q.pdb
# hhsearch
scores_from_program: -999 100.00
7 RIKKKAMELA (…) ESESIKYVIE
5 EIYDAMINGI (…) YSAGQKVTIK
—

And, like I say, the 2h1q.pdb is in the directory and when I open it it seems like a very normal file:

ATOM 1 N PHE A 1 -0.433 28.290 54.674 1.00 88.88 N
(…)
ATOM 1867 OXT LYS A 247 0.587 32.549 77.191 1.00 56.78 O
TER

And, for reference, here’s the fasta file:
>NP_143367.1 gi|14591289|ref|NP_143367.1| hypothetical protein [Pyrococcus horikoshii]
MNGMLLSRIKKKAMELAEDLKLVDFSFGLPYTWVLVEGIEGRALGVAMTLPEEVQRYTNS
IEEPSLLEFIDKADSLNIIERTLGVAAINAVSQYYIDLREAKWIDVTELIQQDEIKRIAI
IGNMPPVVRTLKEKYEVYVFERNMKLWDRDTYSDTLEYHILPEVDGIIASASCIVNGTLD
MILDRAKKAKLIVITGPTGQLLPEFLKGTKVTHLASMKVTNIEKALVKLKLGSFKGFESE
SIKYVIEV

If you have any further ideas of how to edit the alignment file, let me know.

Thanks!!