[modeller_usage] Using an alignment object in automodel

[Will Dampier <>]

Hello all,
I was wondering if there was a trick to using an alignment object
produced by alingment.salign() in an automodel.
My current method writes the alignment to a file and then re-reads it
with automodel.  This is extremely clunky but based on the docs it
seems the only way to go.

Current Example:

env = environ()
aln = alignment(env)
mdl = model(env, file = '1OPN') #The pdb model I'm using for this example.
aln.append_model(mdl, align_codes = '1OPN', atom_files = '1OPN')
aln.append(file = 'hiv.fasta', align_codes = 'all', alignment_format = 'fasta')

aln.salign(gap_function = True)

aln.write('tempfile.ali') #write the file

a = automodel(env, alnfile = 'tempfile.ali', sequence = 'hiv', knowns
= '1OPN') #read it back in
a.make()



As I expand this using the parrellel toolbox it becomes difficult to
manage filenames, etc.  If there was a way to just pass in the
alignment object to automodel then life would be much easier.



Thanks for the help

Will