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