Hi Ben,

Problem solved. Apparently, the problem was about the offset. The second DNA strand, although belonging to a different PDB chain,
has the first resid at 251 (in my case), so IMP complained about the offset with the FASTA. By applying an offset of -250 it is working.

A question related to the issue: IDEAL_HELIX only works when creating the molecule from scratch? (e.g. State.create_molecule(mol).add_representation(ideal_helix=True))



On Wed, 2 Mar 2022 at 19:37, Ben Webb <ben@salilab.org> wrote:
On 3/2/22 1:57 AM, Altair Hernández wrote:
> When using IMP.pmi, I find that the output PDB models for the DNA
> replace the base pairs by Alanines (ALA) for one of the DNA strands.
> Instead, for the other strand it keeps it as original. Why could this be
> happening?

Without seeing your input files, it's impossible to say for sure. But
the first thing to check would be that you're telling PMI your sequence
is DNA when you read it in. If you're using a topology file, add ",DNA"
to the end of the FASTA ID:

If you're creating the structure programmatically using
State.create_molecule, set alphabet=IMP.pmi.alphabets.dna:

ben@salilab.org                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
        - Sir Arthur Conan Doyle