[phenixbb] PHENIX refine: detached sidechain atoms

Vellieux Frederic Frederic.Vellieux at ibs.fr
Thu Jun 24 02:41:16 PDT 2010


Hi,

Can't you go to Coot before refining, and in the Model/Fit/Refine menu 
use either "Real Space Refine Zone" or "Regularize Zone" (I suspect the 
former preferred) on the residues that cause problems, before trying 
Phenix refinement again? I'd try to do that first...

Fred.

Oliver King wrote:
> Hi All,
>
> I've noticed that when refining a model in phenix.refine using a PDB 
> file from Refmac, the sidechain atoms of certain residues become 
> detached from the rest of the molecule and appear to float on their 
> own, at least when viewing in Coot. I think this is down to the format 
> of the PDB file. For example the atoms of a Leu residue from a 
> phenix.refine file which displays well is of the form:
>
> ATOM      1  N   LEU A   8      50.022 -34.247  -5.817  1.00 
> 58.12           N
> ATOM      2  CA  LEU A   8      49.788 -34.905  -4.539  1.00 
> 55.84           C
> ATOM      3  C   LEU A   8      48.339 -35.358  -4.348  1.00 
> 60.39           C
> ATOM      4  O   LEU A   8      48.008 -36.016  -3.360  1.00 
> 68.40           O
> ATOM      5  CB  LEU A   8      50.219 -34.011  -3.373  1.00 
> 57.98           C
> ATOM      6  CG  LEU A   8      51.690 -34.126  -2.975  1.00 
> 65.66           C
> ATOM      7  CD1 LEU A   8      52.014 -33.170  -1.836  1.00 
> 59.99           C
> ATOM      8  CD2 LEU A   8      52.020 -35.566  -2.594  1.00 
> 68.57           C
>
> where as from a Refmac PDB which also behaves well, it is of the form:
>
> ATOM      1  N   LEU A   8      50.453 -35.722  -5.617  1.00 
> 20.00           N
> ATOM      2  CA  LEU A   8      49.649 -35.131  -4.482  1.00 
> 20.00           C
> ATOM      3  CB  LEU A   8      50.190 -33.735  -4.147  1.00 
> 20.00           C
> ATOM      4  CG  LEU A   8      51.461 -33.755  -3.275  1.00 
> 20.00           C
> ATOM      5  CD1 LEU A   8      52.556 -32.768  -3.741  1.00 
> 20.00           C
> ATOM      6  CD2 LEU A   8      51.082 -33.546  -1.799  1.00 
> 20.00           C
> ATOM      7  C   LEU A   8      48.166 -35.063  -4.824  1.00 
> 20.00           C
> ATOM      8  O   LEU A   8      47.822 -34.257  -5.568  1.00 
> 20.00           O
>
> but after refinement in phenix it becomes
>
> ATOM      1  N   LEU A   8      50.734 -35.936  -5.935  1.00 
> 54.45           N
> ATOM      2  CA  LEU A   8      49.846 -35.185  -4.892  1.00 
> 51.89           C
> ATOM      3  CB  LEU A   8      50.377 -33.761  -4.516  1.00 
> 51.22           C
> ATOM      4  CG  LEU A   8      51.550 -33.730  -3.431  1.00 
> 59.27           C
> ATOM      5  CD1 LEU A   8      52.457 -32.407  -3.635  1.00 
> 60.88           C
> ATOM      6  CD2 LEU A   8      51.120 -34.090  -1.879  1.00 
> 55.50           C
> ATOM      7  C   LEU A   8      48.268 -35.042  -5.221  1.00 
> 47.92           C
> ATOM      8  O   LEU A   8      47.989 -34.282  -6.195  1.00 
> 47.32           O
>
> and the CD2 atom is now too far away to be part of the residue in Coot
>
> Is there an easy way to convert a PDB from Refmac into one which will 
> behave itself when put through phenix.refine? I've tried using 
> phenix.pdb_tools and also putting the model through Molprobity and 
> hoping that that the output would be corrected.
>
> Thanks,
>
> Olly King
>
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