I would appreciate some input.
Best regards.
On Mon, Sep 2, 2019 at 7:00 PM Ahmad Khalifa underoath006@gmail.com wrote:
> Hello, > > I have two sequences with low sequence identity and I get an alignment in > modeller different than clustalW, which also differs from when I use emboss > matcher. > > I also have a missing segment in my template, I want the final model to > have the corresponding segments and the gaps unmodeled, same as the > template. > > I tried to modify the alignment manually, however I ran into the > "SequenceMismatchError: read_te_291E> Sequence difference between alignment > and pdb :" error, which I think has to do with the number of residues in > the header of the alignment. > > I attached the modeller and matcher alignments, in pir and fasta > respectively. I would appreciate if you tell me how to prevent the missing > loops in the template from being built and how to modify the alignment > manually bypassing the above error. > > Also, do give your input regarding the difference in alignments, and how > to choose the most accurate one. I'm also fine with sharing the files > privately. > > Best regards. > > >