[ccp4bb]: refmac question

["Rife, Chris" <chris.rife@Vanderbilt.Edu>]

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Hi,

I am trying to refine a structure with Mn using refmac but am having some
difficulty. I start with a pdb which contains the following:

.....
ATOM   2126  OXT ALA B2134      32.150  12.226  -9.111  1.00 33.13      BBBB
ATOM   2127  K   K   C3001      37.078   5.878  11.104  1.00 34.02      CCCC
ATOM   2128  K   K   C3002      37.925  39.486  12.588  1.00 26.80      CCCC
ATOM   2129 MN   MN  C3003      34.539  11.900  12.205  1.00 14.23      CCCC
ATOM   2130 MN   MN  C3004      36.301  33.497  14.694  1.00 12.66      CCCC
ATOM   2131  O   HOH D9001      37.913  36.563  13.237  1.00 33.46      DDDD
ATOM   2132  O   HOH D9002      20.851  38.818  10.123  1.00 19.39      DDDD
ATOM   2133  O   HOH D9003      27.208   6.387  17.974  1.00 14.02      DDDD
.....

Then I run a round of refmac (either alone, or with arp_warp), and I end up
with:

.....
ATOM   4162  OXT ALA B2134      31.181  12.907  -9.047  1.00 46.81           O
ATOM   4163  K   K   C3001      36.729   5.970  11.161  1.00 34.89           K
ATOM   4164  K   K   C3002      37.470  39.816  12.520  1.00 29.67           K
ATOM   4165 MN   MN  C3003      34.244  11.984  12.190  1.00 31.90          MN
ATOM   4166  O6  .       0      35.180  10.408  10.686  1.00123.91           O
ATOM   4195  O   HOH D9002      20.517  39.123  10.155  1.00 18.29           O
.....

Somehow my second Mn has been and the first water are both lost. I am using ccp4
4.2, and this occurs on different both SGI and MacOSX. Any suggestions?

Thanks,
Chris

Department of Biochemistry
Vanderbilt University
Nashville, TN 37232