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))

Thanks!

Altair

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: > > https://integrativemodeling.org/2.16.0/doc/ref/classIMP_1_1pmi_1_1topology_1... > > If you're creating the structure programmatically using > State.create_molecule, set alphabet=IMP.pmi.alphabets.dna: > > https://integrativemodeling.org/2.16.0/doc/ref/classIMP_1_1pmi_1_1topology_1... > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >