Dear all,
I am searching for methods to replace the fragment. I have a model and a fragment of this protein from experiment. I would like to replace the corresponding part on the model(green) with the fragment(cyan). I also wanted the ligand/molecule attached to the fragment remain attached after replacement. Is there any way to do it?
Thanks for helping
PyMOL is not really the proper tool to do this, as you need to do at the very least some energy minimisation/regularization of bond lengths and angles at the splice site.
UCSF ChimeraX https://www.cgl.ucsf.edu/chimerax/ would be a more suitable free tool.
Hi,
align both models in chimera (Tools > Structure Comparison > MatchMaker / Match align) and saved both models in a single file. Open that file in a text editor (notepad or Wordpad) and delete/replace the green with the cyan part.
I hope that the chimera will recognize the bonds, but if not, then you can create them manually (Tools > structure editing).
Finally, you need to minimize the final structure that can be done in chimera (it is available in Tools as well).
- Badges
- Science topic
- Similar topics
- Philosophy
- Esthetics
- Interpretation