Re: [IMP-users] DNA modeling

[Ben Webb <>]

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_1TopologyReader.html

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_1State.html#a6448c3de07edc1ad3fd58e139aca924a

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