Hey,

at the first and second line of your alignment file (.ali), there should be something like

>P1;sequence name

::: sequence name ... blablabla

this sequence name must match with the align_code in your python script.

Cheers,

Ali

How can I assist you? Do you need to do your homology medel of your targeted protein?

Thanks,

Abu Saim Mohammad Saikat

Ali Osman Acar Thanks

Abu Saim Mohammad Saikat No brother. I am trying to do it by myself. By the way Thanks.

I have faced similar issue. In my case, the problem happened when I did select single sequence as the template. In script two the commands are--

from modeller import *

env = Environ()

aln = Alignment(env)

for (pdb, chain) in (('tseq1', 'A'), ('tseq2', 'A')):

m = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))

aln.append_model(m, atom_files=pdb, align_codes=pdb+chain)

aln.malign()

aln.malign3d()

aln.compare_structures()

aln.id_table(matrix_file='family.mat')

env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0)

>>>here if you use only template sequence python can't understand and creates problem in determining TUPLES (Reference: Biostar), therefore you need to select multiple sequence with accurate Chain >>A or B or whatever.

Again, script 3 is here--

from modeller import *

env = Environ()

aln = Alignment(env)

mdl = Model(env, file='tseq1', model_segment=('FIRST:A','LAST:A'))

aln.append_model(mdl, align_codes='tseq1', atom_files='tseq1.pdb')

aln.append(file='qseq1.ali', align_codes='qseq1')

aln.align2d()

aln.write(file='qseq1-tseq1.ali', alignment_format='PIR')

aln.write(file='qseq1-tseq1.pap', alignment_format='PAP')

>>here, in the mdl line (mdl = Model.........), you need to select the best template what you think or suppose, for e.g. tseq1 for my case, it can be template sequence 3 or 4 in your case, then you need to determine the chain FIRST: ?? A or B or C or Whatever , for your supposed best probable template.

the script 4 will be:

from modeller import *

from modeller.automodel import *

#from modeller import soap_protein_od

env = Environ()

a = AutoModel(env, alnfile='qseq1-tseq1.ali',

knowns='tseq1', sequence='qseq1',

assess_methods=(assess.DOPE,

#soap_protein_od.Scorer(),

assess.GA341))

a.starting_model = 1

a.ending_model = 3

a.make()

like this. The Modeller will generate 3 models for me as I have indicated a.ending_model = 3 above.

All of these things have been discussed easily in that youtube video, Link:

(312) Modelling proteins using Modeller 9.10 [Homology Modelling] - YouTube

Video length: 42.41 minute

Channel: avip04

Published date: Jan 26, 2012

If you still face problems, please let me know. I am confident to solve this problem, as I have gone through this same difficulty>> [email protected]

Thank You Very Much, Good Luck.