[phenixbb] A few questions

Peter Zwart PHZwart at lbl.gov
Wed Feb 6 09:02:20 PST 2008


I guess what is needed is not individual occupancy refinement, but
'grouped' occupancy refinement:

http://www.phenix-online.org/documentation/refinement.htm#anch106

HTH

Peter

2008/2/6, Paul Adams <PDAdams at lbl.gov>:
> Hi Pavel,
>
>    the occupancy should be the same for all of the atoms in an
> alternate conformation (grouped occupancy refinement). I doesn't make
> chemical sense for bonded atoms to have different occupancies.
>
>    Cheers,
>         Paul
>
> On Feb 6, 2008, at 8:56 AM, Pavel Afonine wrote:
>
> > Hi Christopher,
> >
> > thanks for your questions!
> >
> >> We are working on a refinement at 1.14A which was suffering from
> >> lots of NPD atoms when refined anisotropically with refmac5 and/or
> >> shelx.
> >
> > The implementation of anisotropic B-factors refinement in
> > phenix.refine
> > should never lead to non-positive definite ADP matrices or any
> > "instability" in refinement.
> >
> >> 1. In our model we have a few solvent ligands, and these show up
> >> in the log file as:
> >>           Unusual residues: {'EDO': 11, ' CL': 1, 'SO4': 1}
> >>           Classifications: {'undetermined': 13, 'water': 437}
> >> We've used a cif file for EDO with H's when needed, but still see
> >> this message. Is this normal? What is unusual?
> >>
> >
> > Yes, it is normal. In this context "unusual" means that this is not
> > "usual amino acid, water, dna/rna fragment".
> >
> >> 2. When choosing "indivdual_occupancies" for the refinement, all
> >> the atoms within an alt-conf are refined to different occupancies-
> >> is this expected? It seems that all atoms in the A conf should
> >> have the same value, and the occ of all atoms in the B conf should
> >> also be the same. Instead, we see this:
> >> ATOM    232  CA AGLU A  28      26.163   7.163   4.422  0.77
> >> 6.73           C
> >> ATOM    233  CB AGLU A  28      24.851   7.269   3.672  0.80
> >> 9.27           C
> >> ATOM    234  CG AGLU A  28      24.978   6.767   2.259  0.66
> >> 12.91           C
> >> ATOM    235  CD AGLU A  28      23.662   6.717   1.554  1.00
> >> 16.51           C
> >> ATOM    236  OE1AGLU A  28      22.874   7.667   1.757  0.71
> >> 18.78           O
> >> ATOM    237  OE2AGLU A  28      23.429   5.733   0.803  0.60
> >> 16.77           O
> >> ATOM    240  CA BGLU A  28      26.140   7.156   4.424  0.23
> >> 6.33           C
> >> ATOM    241  CB BGLU A  28      24.794   7.230   3.713  0.20
> >> 6.48           C
> >> ATOM    242  CG BGLU A  28      24.877   6.766   2.280  0.34
> >> 6.55           C
> >> ATOM    243  CD BGLU A  28      23.536   6.702   1.598  0.00
> >> 7.53           C
> >> ATOM    244  OE1BGLU A  28      23.497   7.014   0.381  0.29
> >> 7.85           O
> >> ATOM    245  OE2BGLU A  28      22.543   6.341   2.280  0.40
> >> 8.40           O
> >>
> >
> > This is correct behavior and this is exactly what you should expect
> > refining occupancies of atoms in alternative conformations: the sum of
> > occupancies of conformation A and B must be one. So, in your
> > example above:
> >
> > ATOM 232 CA AGLU A 28 26.163 7.163 4.422 0.77 6.73 C
> > ...
> > ATOM 240 CA BGLU A 28 26.140 7.156 4.424 0.23 6.33 C
> >
> > the total occupancy is: 0.77+0.23=1
> > Same for other atoms.
> >
> >> 3. Adding hydrogens during anisotropic refinement results in the
> >> Parvati server giving "Illegal Biso" errors for many of the
> >> hydrogens.
> >
> > The H atoms at normal resolutions (not subatomic resolution) are
> > treated
> > as a special case. For example (default behavior), they ride on bonded
> > atoms during coordinates refinement (riding model, distances X-H do
> > not
> > change), we refine one occupancy and isotropic B-factor per all H
> > atoms
> > in your molecule, etc. I don't know what exactly "Illegal Biso"
> > means in
> > Parvati server, but most likely you want to exclude H atoms for this
> > analysis.
> >
> > Just a suggestion: at resolution 1.4A you can try to change the
> > default
> > behavior for H refinement to this:
> >
> >   hydrogens {
> >     refine_adp = *one_b_per_residue one_b_per_molecule individual
> >     refine_occupancies = *one_q_per_residue one_q_per_molecule
> > individual
> >   }
> >
> > Please let us know if you have any questions or problems!
> > Pavel.
> >
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> --
> Paul Adams
> Deputy Division Director, Physical Biosciences Division, Lawrence
> Berkeley Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Head, Berkeley Center for Structural Biology
>
> Building 64, Room 248
> Tel: 510-486-4225, Fax: 510-486-5909
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
> --
>
>
>
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