[phenixbb] PHENIX refine: detached sidechain atoms - SOLUTION

Pavel Afonine PAfonine at lbl.gov
Thu Jun 24 22:22:02 PDT 2010


Hi Oliver,

thanks for sending the inputs so we could reproduce this issue and 
figure out what is wrong.

The problem maker is the CIF file for your ligand that specifies 
unrealistic (too small) esds for some torsional angles that in turn 
creates huge terms in geometry restraints target that finally resulted 
in a huge X-ray weight. Using huge X-ray weight obviously means that you 
are doing nearly unrestrained refinement and therefore no surprises that 
the geometry was systematically distorted. This is something we will be 
catching automatically in future, but meanwhile it is a good idea to use 
correct ligand CIF files.

The solution: create a CIF file using either phenix.elbow or, better, 
using phenix.ready_set commands. For example,

phenix.ready_set model.pdb

will create a CIF file for all ligands in your model.pdb file. Using 
this file in refinement eliminates the problem that you have reported 
this morning. Also, this command adds H atoms to model.pdb file, that 
you can then use in subsequent refinements.

I went ahead some more and did some refinement using the strategy that I 
think is the best for your case.

Your starting R-factors (corresponding to the model you sent me):
r_work = 0.1853 r_free = 0.2523 bonds = 0.069 angles = 4.460

And after some refinement that I've done:
r_work = 0.1779 r_free = 0.2202 bonds = 0.015 angles = 1.600

In refinement I used:
- automatic water update;
- TLS;
- riding hydrogen atoms.

You can further improve your model by:
- running automatic rotamer fixing (fix_rotamers=true);
- weights optimization (optimize_wxc=true optimize_wxu=true);
- more thoughtful selection of TLS groups.

I'm sending to you all the files OFFLIST (in the next email).

Please let me know if you have any questions.

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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