Hello,

If i have the following alignment

>P1;1ji4
structureX:1ji4:FIRST:A:LAST:A::::
MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEI---------Y
EEFADMFDDLAERIVQLGHHPLVTLSEAIKLTRV-----KEETKTSFHSKDIF
KEILEDYKYLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHL--
-----A*


>P1;madeup
sequence:madeup:::::::
-------------------------------------------MSFIEKMIGS
LNDKREWKAMEARAKAL---PKEYHHAYKAIQKYMWTSGG--PTDWQDTKRIF
GGILDLFEEGAAEGKKVTDLTGE--D--VAAFCDELMKDTKTWMDKYRTKLND
SIGRD-*

and i want to transfer the coordinates from my template to my sequence without building the loops. How should I change my code so it would do that for me??

This is the code that i have been using.

from modeller import *

env = environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

aln = alignment(env, file='alignment.ali',align_codes=('1ji4', 'madeup'))
mdl = model(env)

mdl.generate_topology(aln['madeup'])

# Assign the average of the equivalent template coordinates to MODEL:
mdl.transfer_xyz(aln)

# Get the remaining undefined coordinates from internal coordinates:
mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')

# Write the final MODEL coordinates to a PDB file:
mdl.write(file='madeup.pdb')

Regards,
Ali Algarrous