[phenixbb] Electrostatic potential map/Delphi/PDB2PQR

Pavel Afonine pafonine at lbl.gov
Tue Oct 21 08:33:58 PDT 2014

Hello Ivan,

> 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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