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