[phenixbb] "H" atom refining occupancy with previous altconf residue in sequence

Alexander Scouras scouras at berkeley.edu
Thu Oct 25 20:05:22 PDT 2012


After a series of residues (1+) with alternate conformations, the H atom of the next residue seems to lock its occupancy to that of the final conformation of the previous residue.  Hence I'm getting several H's with 0.1-0.5 occupancy on single conformation residues, where the entire rest of the residue has occupancy 1.  This happens after every altconf series, and showed up in two separate structures I've worked on this week.

Within a series of 2+ residues with altconfs, the H's refine correctly with their altconf groups.  So it isn't just that all subsequent residue's H's are getting overridden.

This behavior seems to have started with 1.8.1-1168, or at least previous refinements of the same structure didn't do this.  64 bit build on Retina MBP running OS X 10.8.2.

I couldn't google any reference to this behavior, so assuming it's a new bug I can send along source files.

Below I've pasted a couple residues from one of my PDBs.  I added a ***** to mark the offending H with the wrong occupancy. 

-Alex Scouras





ATOM    668  N  CMET A  29     -17.970   6.464  59.720  0.21 10.72           N
ANISOU  668  N  CMET A  29     1641   1300   1133   -328   -379    -50       N
ATOM    669  CA CMET A  29     -17.578   5.189  60.316  0.21  9.05           C
ANISOU  669  CA CMET A  29     1545    882   1012   -248   -350   -140       C
ATOM    670  C  CMET A  29     -17.248   5.317  61.797  0.21  7.83           C
ANISOU  670  C  CMET A  29     1363    666    947    173   -134    166       C
ATOM    671  O  CMET A  29     -17.496   4.395  62.578  0.21  7.92           O
ANISOU  671  O  CMET A  29     1187    751   1071    371   -145    338       O
ATOM    672  CB CMET A  29     -16.376   4.609  59.573  0.21  9.09           C
ANISOU  672  CB CMET A  29     1561    834   1059   -243   -283   -203       C
ATOM    673  CG CMET A  29     -16.681   4.210  58.145  0.21  9.05           C
ANISOU  673  CG CMET A  29     1529    756   1154    -28   -331   -235       C
ATOM    674  SD CMET A  29     -18.049   3.042  58.009  0.21 13.05           S
ANISOU  674  SD CMET A  29     2356   1325   1279   -218   -284    -50       S
ATOM    675  CE CMET A  29     -17.505   1.757  59.124  0.21 12.06           C
ANISOU  675  CE CMET A  29     1866   1485   1232   -630   -667    420       C
ATOM    676  H  CMET A  29     -17.333   6.878  59.318  0.21 12.87           H
ATOM    677  HA CMET A  29     -18.320   4.557  60.216  0.21 10.86           H
ATOM    678  HB2CMET A  29     -15.671   5.275  59.551  0.21 10.91           H
ATOM    679  HB3CMET A  29     -16.069   3.819  60.044  0.21 10.91           H
ATOM    680  HG2CMET A  29     -16.916   5.004  57.640  0.21 10.86           H
ATOM    681  HG3CMET A  29     -15.894   3.794  57.761  0.21 10.86           H
ATOM    682  HE1CMET A  29     -18.164   1.059  59.140  0.21 14.48           H
ATOM    683  HE2CMET A  29     -16.666   1.409  58.813  0.21 14.48           H
ATOM    684  HE3CMET A  29     -17.401   2.130  60.002  0.21 14.48           H
ATOM    685  N   MET A  30     -16.667   6.445  62.187  1.00  6.77           N
ANISOU  685  N   MET A  30     1361    564    647    -30    -56     18       N
ATOM    686  CA  MET A  30     -16.416   6.699  63.606  1.00  7.66           C
ANISOU  686  CA  MET A  30     1362    946    601    -42   -173      2       C
ATOM    687  C   MET A  30     -17.759   6.724  64.367  1.00  7.62           C
ANISOU  687  C   MET A  30     1310    944    641     -9    -24    -22       C
ATOM    688  O   MET A  30     -17.852   6.212  65.486  1.00  9.05           O
ANISOU  688  O   MET A  30     1571   1151    718     84     98    231       O
ATOM    689  CB  MET A  30     -15.620   7.987  63.790  1.00  7.65           C
ANISOU  689  CB  MET A  30     1299    894    714     26   -120   -166       C
ATOM    690  CG  MET A  30     -14.229   7.965  63.231  1.00  8.62           C
ANISOU  690  CG  MET A  30     1464   1072    741     31   -163    -10       C
ATOM    691  SD  MET A  30     -13.130   6.745  64.006  1.00  9.04           S
ANISOU  691  SD  MET A  30     1555    961    919    105   -180    -94       S
ATOM    692  CE  MET A  30     -12.812   7.527  65.563  1.00  9.77           C
ANISOU  692  CE  MET A  30     1540   1284    889    150   -190    -62       C
ATOM    693  H   MET A  30     -16.395   7.062  61.653  0.21  8.12           H      *****
ATOM    694  HA  MET A  30     -15.872   5.965  63.962  1.00  9.19           H
ATOM    695  HB2 MET A  30     -16.099   8.709  63.352  1.00  9.18           H
ATOM    696  HB3 MET A  30     -15.550   8.173  64.739  1.00  9.18           H
ATOM    697  HG2 MET A  30     -14.278   7.758  62.284  1.00 10.35           H
ATOM    698  HG3 MET A  30     -13.831   8.840  63.354  1.00 10.35           H
ATOM    699  HE1 MET A  30     -12.228   6.968  66.079  1.00 11.73           H
ATOM    700  HE2 MET A  30     -12.397   8.378  65.406  1.00 11.73           H
ATOM    701  HE3 MET A  30     -13.644   7.648  66.026  1.00 11.73           H


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