from modeller import *
from modeller.automodel import *
env = environ()
a = automodel(env, alnfile='alnPrev.pir',
knowns='2ks9', sequence='FPR1',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 1
a.make()
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 1", chain " A";
atom file name: 2ks9.pdb
read_te_288W> Protein not accepted: 1 2ks9
It seems like it can't find residue number 1 but I think I can see it.. And when I'm changing the PIR file in the structure line from 1 to first I get the following error:
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 1)
Alignment MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWI
PDB DNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWII
Match ** * * ** *
Alignment residue type 11 (M, MET) does not match pdb
residue type 3 (D, ASP),
for align code 2ks9 (atom file 2ks9), pdb residue number "2", chain "A"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 2ks9