[phenixbb] A few questions

Rife, Christopher L crife at slac.stanford.edu
Wed Feb 6 08:27:35 PST 2008


Hi,

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. We followed the guidelines recently posted to this BB, and initially the results looked pretty good, but upon close inspection we have a few questions.

We are using Version: 2008_01_09_2058.

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?

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

3. Adding hydrogens during anisotropic refinement results in the Parvati server giving "Illegal Biso" errors for many of the hydrogens. 

I can make the files available if that will help.

Thanks,
Chris

-----------------------------------------
Structure Determination Core
Joint Center for Structural Genomics
Stanford Synchrotron Radiation Laboratory
 




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