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On 28/06/11 12:13, Katrina L Molland wrote: > I am trying to use Coot to change the numbering of the residues in a PDB file. The structure contains six semi-identical lettered chains, currently described as D through I. For some reason, the feature in coot that should allow me to change them to A-F, as well as change the residue numbering, will only allow me to alter the first chain. Any ideas? The only other solution I can think of is to directly alter the text of the PDB file, but the tedious nature of the task and the possibility of introducing mistakes makes it rather unattractive. So, IIUC, you can change D -> A, but E -> B fails. E -> B should fail if there is a B chain already - even if it has only one atom in it. If there is no B chain, then E -> B should work. If it does not work you may well have discovered a bug. What does the console say? You might like to try the following (Calculate -> Scripting -> Scheme): (change-chain-id 0 "B" "E" 1 1 999) Where the 0 is the molecule number of the model you are trying to modify - you might need to change that and 999 is the last residue number in the chain - you might need to modify that too. Paul.