On 11 Nov 2022, 19:46, Murpholino Peligro wrote:
Can hydrogens be added in a pH/pka-dependent manner? Something like this
(https://server.poissonboltzmann.org/) but get a pdb file ready for
phenix.refine/buster/refmac?
You might want to try http://newbiophysics.cs.vt.edu/H++/. It outputs an
updated PDB file that could be fed to a refinement program.
The reduce code (from the molprobity folks) does much the same thing, but
not in a pH-dependent fashion. Still, it might be worth comparing to H++:
none of these predictors is fully accurate, and intuition (or agreement with
experiment) often needs to be considered as well.
....dave case
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