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