You can rename atoms (or residues) in COOT one by one But being old fashioned I would probably use an editor.. Save all the ions in a new coordinate list.. Note what you want to rename them to. Edit the coordinates appropriately, then merge after the renaming is done!
On Wed, 13 Aug 2025 at 10:49, Christian Steinmetzger < [email protected]> 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. > > 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 > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
