[phenixbb] PHENIX refine: detached sidechain atoms

Pavel Afonine PAfonine at lbl.gov
Thu Jun 24 06:46:28 PDT 2010


Hi Oliver,

this is not expected to happen, and you don't need to do anything with 
your PDB file to run it with phenix.refine.

Can you send me the inputs for your refinement run (model, data and the 
command including parameter file(s) is any) so I can reproduce this 
behavior myself and explain what happens? At this point I have too 
little information about your refinement run, version of PHENIX and so 
on to say something. All files will be used confidentially and for 
addressing this issue only.

Pavel.


On 6/24/10 3:42 AM, 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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