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
>>
>>
>>
>>
>>
>
>
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