Hi Christian, it is not a problem for subsequent refinement and
deposition after all. However I like to have all heteroatoms close to
one chain having the same chain ID. There was a similar question just
asked and you could run in phenix sort heteroatoms groups after merging.
Br, Georg.
Am 13.08.2025 um 11:37 schrieb Christian Steinmetzger:
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.
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.
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.
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.
Cheers,
Christian
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