I want to add missing residue in protein 1g05, which has 2 chains in it namely A and B. Chain A and B are identical (I aligned chain A and Chain B in pymol they aligned nicely.) In chain A the missing residues are 225-227, 252-255 and in Chain B the missing residues are 725-731. How to generate .ali file?

I used the following steps to generate sequence following the tutorial (https://salilab.org/modeller/wiki/Missing%20residues)

from modeller import * # Get the sequence of the 1qg8 PDB file, and write to an alignment file code = '1g09' e = environ() m = model(e, file=code) aln = alignment(e) aln.append_model(m, align_codes=code) aln.write(file=code+'.seq')

Then I got output as follows:

>P1;1g05

structureX:1g05: 83 :A:+332 :B:MOL_ID 1; MOLECULE STROMELYSIN-1 PRECURSOR; CHAIN A, B; FRAGMENT CATALYTIC DOMAIN; SYNONYM MMP-3; EC 3.4.24.17; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; CELL FIBROBLAST; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562: 2.45: 0.25

FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPF

DGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHDLTRFRLS

QDDINGIQSLYGPPPD/FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEA

DIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANT

EALMYPLYHFRLSQDDINGIQSLYGPPPDSPET*