Dear Ben:

Thank you for your advice.

I forgot to mention that the sequence that to be aligned with the other three tempates does not have 3D structure. I have try the way as you suggested. The modeller returned to error message saying that 2c17 does not have a pdb code. Here is what I got:

runcmd______> model.read(file='2c17', (def)model_format='PDB', model_segment=('FIRST:@', 'END:'))

pdbnam__217W> Filename for PDB code not found: 2c17
              Directories: ./:../atom_files/
              Extensions :   :.atm:.pdb:.ent:.crd
openf5__224_> Open       11 OLD SEQUENTIAL file-not-found
openf5__225E> File does not exist: file-not-found

In such case, should I be able to align my sequence to other tempates with known 3D-structures? I have attached my script and the log file as attachments.

Thank you for help.

Bo

Modeller Caretaker <modeller-care@salilab.org> wrote:

Bo Yang wrote:
> 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:'))

You can only read in a single model at a time with 'model'. If you want
to read multiple models, put it in a 'for' loop, just as for the earlier
salign script you used.

Ben Webb, Modeller Caretaker
--
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