[ccp4bb]: SeMet

["David E. Timm" <dtimm@iupui.edu>]

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Hello,

I am trying to refine a structure containing selenomethionine.  The MET
residues are set up as follows in the input pdb file:

ATOM     80  N   MET A  21      24.850  71.566  43.125  1.00 58.39      A
N
ATOM     81  CA  MET A  21      25.712  71.362  41.969  1.00 59.48      A
C
ATOM     82  C   MET A  21      24.919  71.185  40.673  1.00 57.59      A
C
ATOM     83  O   MET A  21      23.863  70.571  40.733  1.00 56.34      A
O
ATOM     84  CB  MET A  21      26.559  70.095  42.036  1.00 59.25      A
C
ATOM     85  CG  MET A  21      27.635  70.081  43.079  1.00 59.63      A
C
ATOM     86 SE   MET A  21      28.604  71.547  43.261  1.00 54.05      A
S
ATOM     87  CE2 MET A  21      29.827  71.529  41.981  1.00 60.88      A
C

I am using the version 4.0 suite, which I thought had a dictionary file
setup for selenomethionine:

 FORMATTED      OLD     file opened on unit   9
 Logical name: DICTPROTN, Full name:
/xtal1/usr/local/ccp4-4/lib/data/protin.dic


                                                 1   13          MET M
  -0.525    -0.780    -1.206                1         5   -1
CB
  -2.039    -0.908    -1.252                1         6   -2
CG
  -2.617    -1.831    -2.688                4         7   -3
SD
  -4.389    -1.785    -2.430                1         8   -4
CE
  -2.652    -1.887    -2.776                4         9   -3
SE
  -4.533    -1.839    -2.502                1        10   -4
CE2


PROTIN runs with the following warning:

 The following Atoms are missing from the deck  of atomic Coordinates ---


 SD   of MET   21
 CE   of MET   21
 SD   of MET  156
 CE   of MET  156
 SD   of MET  198
 CE   of MET  198
 SD   of MET  259
 CE   of MET  259
 OE   of LYSC 262
 OXT  of LYSC 262
 SD   of MET  156
 CE   of MET  156
 SD   of MET  198
 CE   of MET  198
 SD   of MET  259
 CE   of MET  259
 OE   of LYSC 262
 OXT  of LYSC 262


However, my main concern is the fact that REFMAC is using sulfur scattering
factors rather than selenium:

 Logical name: ATOMSF, Full name:
/xtal1/usr/local/ccp4-4/lib/data/atomsf.lib


CIFBEGIN_atomsf


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650
51.6512   0.2156
  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663
0.5826 -11.5290
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670
32.9089   0.2508
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408
57.7997   0.0030
  S      6.2915   2.4386   3.0353  32.3337   1.9891   0.6785   1.5410
81.6937   1.1407
CIFEND

I have changed the column position of the SE atom name in the pdb file, but
get the same S scatter factor.  Any suggestions?  Cheers,  Dave Timm