On 12/5/19 6:39 AM, Lenz, Swantje wrote: > I am building a system using PMI and IMP.pmi.topology.TopologyReader. I > have proteins, DNA and RNA.
You may be the first person to try this so I wouldn't be surprised if you run into issues - IMP's support for nucleic acids isn't well tested. If you can get me a simplified version of your setup so I can reproduce your issues I should be able to fix them.
> If I have A,C,G,U and T in my fasta file I get the following warnings > and errors for DNA.
Looks like IMP's FASTA reader currently assumes all nucleic acids are RNA. But this is easy to fix.
> The script then continues and modeling > proceeds. However, when I try to implement the "deposition" part covered > in https://integrativemodeling.org/tutorials/deposition/, there are > several errors due to not recognizing residue types, since the alphabet > is defined as the peptide alphabet in the ihm module by default.
There's no support for this in PMI currently, unfortunately. But it shouldn't be too difficult to add.
> Additionally, we have two copies of one protein. This causes the second > copy to not be created as an asymmetric unit in create_component in the > protocol output of mmcif.py.
Fixed in git.
Ben