Actually, that was the issue. I manually reset the occupancies of the
problematic atoms in the PDB to unity. This solved my problem.
Thanks to Nat and Tom.
Best,
Chris
On 4/21/14, [log in to unmask] <[log in to unmask]> wrote:
> Hello Chris,
>
> This probably isn't your problem, but I once put some atoms into difference
> density (in Coot) and for some reason the occupancy was set to zero, so
> although everything was refined, the density was the same as before (massive
> difference density). You might want to just check.
> cheers, tom
>
> Tom Peat
> Biophysics Group
> CSIRO, CMSE
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304
> +614 57 539 419
> [log in to unmask]
> ________________________________
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Chris Fage
> [[log in to unmask]]
> Sent: Tuesday, April 22, 2014 8:21 AM
> To: [log in to unmask]
> Subject: [ccp4bb] Trouble Refining Ligand in Phenix
>
> Hi Everyone,
>
> I am trying to refine a structure with a phosphorylated amino acid. After
> refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density
> for all atoms of the derivatized amino acid in Coot, almost as if I had not
> built in the residue. I am loading a .cif for the derivative when I run
> phenix.refine. I have also tried ReadySet, but when I click the "Run in
> phenix.refine" button, I see the message
>
> Error interpreting command line argument as parameter definition:
> "refine_65-coot-2.metal.edits"
> RuntimeError: Unexpected end of output.
>
> Am I just seeing noise, or is Phenix not actually refining this portion of
> the model? I would appreciate any suggestions.
>
> Best,
> Chris
>
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