Hi Eric,
Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would
- delete #1/A:1-10
- select #2/A:1-10, save a pdb file with only the selected residues
- Open this new PDB file (model #3)
- combine #1,3
- Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4
- The I would use the command changechains #4/B A and this would yield the result that I want
What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.
I hope that made it clearer?
Thanks a lot,
Matthias
Hi Matthias,
I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way?
It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.
UCSF Computer Graphics Lab
Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.