[phenixbb] Electrostatic potential map/Delphi/PDB2PQR
pafonine at lbl.gov
Tue Oct 21 08:33:58 PDT 2014
> I am facing a problem. I have a protein-RNA complex at 2A resolution I
> refined using TLS in Phenix. Now in the pdb file I have ANISOU line for
> every atom
these ANISOU records are the result of TLS refinement and not an error.
For example, see
from page 23, if you wish to learn about TLS.
> and probably many other errors.
Specifically, what are these errors?
> This is the reason I am not
> able to run Delphi or PDB2PQR to create potential electrostatic map.
> I removed already all water molecules and all heteratoms and ANISOU
> lines and RNA molecule. The program creating the phi file for the
> potentials does not work at all.
> Do you know any server which can correct any errors in the pdb file
> in order to run properly the program to create electrostatic map ??
I would talk to developers of respective programs. To me it sounds very
odd that you need to do all these weird error-prone manipulations to
your PDB file in order to run these programs.
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