Re: [modeller_usage] alignment of multiple templates

[Bo Yang <>]

Dear Ben:

 

Thank you very much for your help. I fixed the script, and it went through. Now I have a alignment from the three templates.

 

Then I add my sequence to the alignment using the example of 'align.py'. And I have a new alignment (see attachment test.ali). In order to structurally align my sequence with the templates, I try to align the sequence again using the example of "align2d.py". Here is how I tried:

 

env = environ()
env.io.atom_files_directory = "./:../atom_files/"

aln = alignment(env)
mdl = model((env, file=('2HI4-1A2', '1PQ2-2C8A', '1OG5-2C9A'), model_segment=('FIRST:@', 'END:'))
aln.append_model(mdl, align_codes=('2HI4-1A2', '1PQ2-2C8A', '1OG5-2C9A'), atom_files=('2HI4-1A2_fit', '1PQ2-2C8A', '1OG5-2C9A')
aln.append(file='test.ali', align_codes='2c17')
aln.align2d()
aln.write(file='test1a.ali', alignment_format='PIR')
aln.write(file='test1a.pap', alignment_format='PAP')

 

But modeller complained that:

 

mdl = model((env, file=('2HI4-1A2', '1PQ2-2C8A', '1OG5-2C9A'), model_segment=('FIRST:@', 'END:'))

Invalid syntax.

 

Could you please help, how can I align my target sequence with other three templates?

 

Your advices will be very appreciated!

 

Bo

Modeller Caretaker <> wrote:

> Bo Yang wrote:
> > I try to do a multiple structural alignment using the example of 
> > "salign.py" script. The command went through, but the alignment file 
> > only contained the last template sequence. I have attached my script and 
> > the alignment files
>  generated.
>
> You have a bug in your script:
>
> > aln = alignment(env)
> > for (code) in (('2HI4-1A2'), ('1PQ2-2C8A'), ('1OG5-2C9A')):
> > mdl = model(env, file=code, model_segment=('FIRST:@', 'END:'))
> > aln.append_model(mdl, atom_files=code, align_codes=code)
>
> This should read:
>
> > aln = alignment(env)
> > for (code) in (('2HI4-1A2'), ('1PQ2-2C8A'), ('1OG5-2C9A')):
> > mdl = model(env, file=code, model_segment=('FIRST:@', 'END:'))
> > aln.append_model(mdl, atom_files=code, align_codes=code)
>
> i.e. the last line must be indented to line up with the 'mdl = model' 
> line. Indentation is important in Python scripts; the indented line runs 
> within the 'for' loop (and thus for all sequences) while an unindented 
> line runs outside the loop, and thus only for the last sequence.
>
> Ben Webb, Modeller Caretaker
> -- 
>  http://www.salilab.org/modeller/
> Modeller mail list:
>  http://salilab.org/mailman/listinfo/modeller_usage

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Attachment: test.ali
Description: 1655186431-test.ali