Hi ChimeraX team. I am happily using chimeraX along with ISOLDE for modelling. Lately, I am running into issues with complexes having too many chains to be handled by the standard .pdb format which is why I am using .cif now. Is there a smooth way/command to rename chain IDs and change _entity.pdbx_description _struct_asym.entity_id accordingly? Thanks! Kind regards, Dirk -- Dr. rer. nat. Dirk Fahrenkamp UKE Hamburg Zentrum für experimentelle Medizin Institut für Struktur- und Systembiologie/ CSSB Centre for Structural Systems Biology c/o Deutsches Elektronen-Synchrotron DESY Notkestraße 85, Building 15 3.OG D-22607 Hamburg Telefon:+49 (0) 40 8998-87657 Dirk.Fahrenkamp@cssb-Hamburg.de www.cssb-hamburg.de
Hi Dirk, As of tomorrow’s build there will be a non-smooth way to change chain IDs via the ’setattr’ command. For example to change chain A to chain q5: setattr /A c chain_id q5 setattr /A r chain_id q5 You need two commands because in ChimeraX chains are objects in their own right and you can only set their chain ID directly, not by setting the chain ID of one of more of their component residues. So that’s what the first command does. The second command changes the chain ID for miscellaneous residues (ligands, water, other non-polymeric residues) that also have chain ID ‘A’. Also note that if the structure did not originally have any lower case chain IDs but your reassignments result in any lower case IDs, then you will also have to do this: setattr /A st lower_case_chains true Did I mention non-smooth? We intend to implement an easy command for changing chain IDs in the future, but this is what is available (well, actually available as of tomorrow’s build, because the ‘chain_id’ attribute was read only until I changed it a few minutes ago). Also, there are no sanity/safety checks with these commands. If you issue a series of commands and wind up with multiple chains with the same chain ID and residue numbers then Bad Things will happen. AFAIK, writing mmCIF files will pick up the chain ID changes automatically, but I’m not the mmCIF expert on the team. If it doesn’t, just use Help→Report a Bug to file a bug report. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 12, 2020, at 9:31 AM, Fahrenkamp, Dirk <dirk.fahrenkamp@cssb-hamburg.de> wrote:
Hi ChimeraX team.
I am happily using chimeraX along with ISOLDE for modelling. Lately, I am running into issues with complexes having too many chains to be handled by the standard .pdb format which is why I am using .cif now.
Is there a smooth way/command to rename chain IDs and change
_entity.pdbx_description _struct_asym.entity_id
accordingly?
Thanks!
Kind regards, Dirk
-- Dr. rer. nat. Dirk Fahrenkamp UKE Hamburg Zentrum für experimentelle Medizin Institut für Struktur- und Systembiologie/ CSSB Centre for Structural Systems Biology c/o Deutsches Elektronen-Synchrotron DESY Notkestraße 85, Building 15 3.OG D-22607 Hamburg
Telefon:+49 (0) 40 8998-87657 Dirk.Fahrenkamp@cssb-Hamburg.de www.cssb-hamburg.de
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Fahrenkamp, Dirk