I try to do a search for potentially related sequences of known
structure by using the "build_profile.py" from the "command" section of
Modeller9v1. But the program complaines that "Cannot open file
pdb95.fsa: no such files". I search the Modeller9v1 package, and can't
find the file named as "pdb95.fsa".
The pdb95.fsa file is in the examples/commands directory - the same
directory as the build_profile.py script.
Do you know where can I find the "pdb95.fsa" file? Or is there an
alternative file that can be used as the "pdb95.fsa" in the program
package? I notice that there is a file called "pdball.pir" from the
download section of Modeller. Is this one can be used as a database? If
so, how can I change the file format to .fsa?
pdb95.fsa is just all of the PDB sequences, filtered at 95% sequence
identity to remove redundancy. The pdball.pir download from our website
is the same thing. You can convert from PIR to FASTA format using
alignment.read() and alignment.write(), but there is no need, because
profile.read() can also read PIR format databases - just edit
build_profile.py and change seq_database_format from 'FASTA' to 'PIR'.