Sorry - Garib points out form factors are there - labelled atom type
scat cromer ...
You shoulfd find SE if there is a SE atom in the pdb file
Eleanor
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
N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663
0.5826 -11.5290
C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650
51.6512 0.2156
O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670
32.9089 0.2508
SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543
43.8163 2.8409
S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863
56.1720 0.8669
Eleanor Dodson wrote:
I also see such peaks. I have assumed it is because the default in
REFMAC is to use the CuKa SE formfactor, which should be modified at
shorter wave lengths.
(Solution - copy $C:IBD/atomsf.lib and modify Se c to c(CuKa) - f' for
your wavelength.. then assign ATOMSF myversion/atomsf.lib in the
command line
But since now REFMAC has stopped listing the form factors it uses, it
is very hard to know what it has selected or from which library..
You can check whether it is picking up S I suppose by running a job
with MET/SD ad see if there are positive peaks..
Eleanor
Dima Klenchin wrote:
Hello,
I am at a loss on what's going on:
I am refining SeMET containing structure and using REFMAC 5.2.0005 on
Linux and, the same thing happening, using REFMAC 5.5.0070 on Windows.
When MET were modelled, there were no difference peaks anywhere. When
I changed them all to MSE, the large difference density peaks showed
up. So either the protein does not contain SeMet or Refmac somehow
uses sulfur scattering factors during refinement.
I have hard time believing the former because 1) the protein was
checked by mass spec to be correct size for SeMet derivative, 2) the
structure was solved by SAD with all five sites correctly found (196
residues total), 3) first 50 aa of the protein are identical to a
known structure.
This is 2.4A resolution and at this point R/Rfree = 25/29.
Refmac log shows correct scattering factors read out:
SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543
43.8163 2.8409
The PDB has this for MSE:
ATOM 1140 N MSE A 143 35.708 161.163 13.715 1.00
78.82 N
ATOM 1141 CA MSE A 143 35.995 162.467 13.106 1.00
77.86 C
ATOM 1142 CB MSE A 143 36.307 162.307 11.617 1.00
78.79 C
ATOM 1143 CG MSE A 143 37.755 162.127 11.119 1.00
80.89 C
ATOM 1144 SE MSE A 143 37.503 161.104 9.363 1.00
91.22 SE
ATOM 1145 CE MSE A 143 39.169 160.021 9.696 1.00
86.47 C
ATOM 1146 C MSE A 143 34.709 163.226 13.030 1.00
77.70 C
ATOM 1147 O MSE A 143 34.682 164.436 12.737 1.00
77.33 O
Any clues greatly appreciated!
Dima
