To: Help and discussion for users of IMP <>, "Lenz, Swantje" <>
Subject: Re: [IMP-users] mmcif creation with DNA
From: Ben Webb <>
Date: Thu, 5 Dec 2019 10:49:45 -0800
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
--
https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle