Dear Users,
I would like to generate a chimeric protein from templates, especially following the tips from FAQ 1 ( https://salilab.org/modeller/9.10/manual/node36.html) and also here https://salilab.org/modeller/9.10/manual/node21.html.
To better understand the code and its meaning, I used two simple sequences together as test case. In pir file, it has:
>P1;2xkmA structureN:2xkm GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA -------------------------------------------*
>P1;4xknE structureX:4xkh ---------------------------------------------- NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE*
>P1;test sequence:test GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE*
and almost the same for ali file.
However, using the build_profile.py, it shows the first error: _modeller.FileFormatError: parse_pir__E> Invalid PIR file header line: structureN:2xkm There should be 10 fields separated by colons, : This line actually contains 2 fields.
Now here comes my question, from the FAQ, I thought it was enough to use two fields for the template? Even when I put enough colon to make it as 10 fields, it shows the next error that it could not find the PDB file. To fix this problem, I tried to put the entire information of the structureN (and structureX) line from the pdb_95.pir which I download from the Modeller website, with the same build_profile.py, the third error comes: _modeller.StatisticsError: regress_657E> Not enough bins in histogram - cannot calculate statistics, nbins: 1
In the end, I don't understand the exact problem to cause all these errors, did miss something in the pir or ali file? or I used the wrong script. Hope to hear any suggestions from you.
Best wishes.