On 8/31/22 1:15 PM, Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF) wrote: > 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