I am having issues reproducing the Advanced Tutorial provided at https://salilab.org/modeller/tutorial/advanced.html I could not figure out how to write/fix a script to align the 1emd_bs.pdb template with the TvLDH model previously obtained.
An alignment is just a text file, so you can create it using Modeller's alignment functions, some other alignment program, or even by hand in a text editor. I believe that for this particular alignment it was indeed made manually. The sequence identity is so high that it's easy to align visually.
Python script to align template to the model:
from modeller import *
env = Environ()
aln = Alignment(env)
mdl = Model(env, file='1emd_bs', model_segment=('78','94'))
aln.append_model(mdl, align_codes='1emdA', atom_files='1emd.pdb')
aln.append(file='TvLDH-mult.ali', align_codes='TvLDH')
env.io.hetatm = True
aln.align2d(max_gap_length=50)
This won't work because Modeller alignments by default are global. Since 1emd is so much shorter than TvLDH, it will add a lot of huge gaps to try to stretch the sequence out to match. You would want to ask for a local alignment instead.
Ben Webb, Modeller Caretaker
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