how do i align two protein structures one with better resolution (but open form with no ligand) and another with transition state analogue residues (but worse resolution) and connect them this way that i change binding site residues only according to transitional state analogue protein model in structure with better resolution? Do i need to preprosess proteins before the alignment? I'm using maestro.
Indeed you can use swapaa module of UCSF Chimera. Swapaa replaces the same or mutated amino acids.
Use command swapaa leu #0:248.a
here leu represent the new amino acid, 0 represent the model number of the protein, 248 represents the amino acid residue which is needed to be replaced and a represents chain A
(=> - replace amino acid residue 248 in chain A of model 0 with leucine)
For more detail follow the below mentioned link:
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html
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