[phenixbb] PHENIX refine: detached sidechain atoms

Ed Pozharski epozh001 at umaryland.edu
Thu Jun 24 06:23:38 PDT 2010


The CG-CD2 bond is too long after phenix refinement and coot treats it
as broken.  Unless you have ultrahigh resolution, covalent bonds must be
restrained, and expected value for GG-CD2 is 1.521A.  It's 1.53A and
1.54A in your "good" examples, so coot shows the covalent bond.  Then
something happens during refinement and phenix.refine fails to maintain
the correct bond length, it goes up to 1.65A, which is ~4 times more
than standard deviation expected for this bond in monomer libraries.
Accordingly, coot shows this as a broken bond.  You may want to tighten
up the restraints - make sure that your RMSDbonds stays below 0.02A.

No PDB conversion program will fix it as there are no format errors.

Cheers,

Ed.

On Thu, 2010-06-24 at 11:42 +0100, 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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"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs




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