On 13/08/2025 10:37, Christian Steinmetzger wrote:
Hi all,
I'm working on a handful of ribosome structures, around 140000 atoms (no waters
placed yet) with chains A-U, X-Z, a-z, 0-4 and want to place Mg2+ and K+ ions
now after having refined the RNA and protein chains.
To make life easier I wanted to start from existing ion placements in reference
structures such as PDB: 7K00 or 8EMM, which I have aligned to my own models and extracted
the ions. My plan was now to load both my model and the reference ions into Coot, step
from ion to ion, check the fit to density and adjust if needed. Next use "Merge
Molecules..." to combine the ions and my model into a single structure, place waters
and do a final refinement of the whole system.
ok, I am following...
However, the merging isn't going as expected. The chain IDs match between my
structures and the references, e.g. 16S rRNA is chain A and the Mg2+ ions
associated with that RNA are chain A as well. On merging, Coot assigns new
chain IDs to the ions, namely U, V and then a number of chains with blank IDs.
This I did not expect. Yes, I expected a new chain id, but I did not
expect more than one chain id. The input Mg2+ model has only one chain?
How many residues?
Ions that used to be in the same chain in the reference structure are split
between different chain IDs now, and the same chain sometimes also has ions
that are associated with different ribosome chains.
Even if the merge was correct, you would need to rename chain id to
bring the Mgs into the expected/correct chain. Possibly needs a
renumber-residues before that.
Maybe it's easier to do in an editor as Eleanor suggest. Maybe not with
mmcif though.
This seems a bit messy and problematic. Is there a better workflow to get the
ions merged into the ribosome or is this no problem for subsequent refinement
and deposition after all?
This is all done in Coot 0.9.8.95 (Ubuntu) or 0.9.8.96 (MacOS) from CCP4.
OK.
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