Dear Vera,
In my experiences I had no problems to link protein atoms to a ligand in
Coot. Did you check that you merged the cofactor to the protein molecule
first? otherwise that could be one reason why Coot is not creating the link.
BW,
D
On 13/07/2021 14:33, Vera Pfanzagl wrote:
Hello,
I am trying to refine a heme protein which has the heme cofactor
covalently linked to the protein at three positions (two ester
linkages and a sulfilimin bond) (coot.png shows the atoms which should
be in the sulfilimin bond). However as as coot cannot covalently link
atoms between a cofactor and amino acids the atoms are displaced
during the refinement and I don't know how to fix this. Also the heme
b disintegrates if I run it through phenix and then try to refine it
manually in coot. The hydrogen atoms just fly off. I can delete the
hydrogens before running a manual refinement but this problem
reappears after adding the hydrogens during phenix refine.
I now tried to replace it with HEB from the coot monomer library (I
cannot find the old HEM in the monomer library) and got once the same
result (atoms are displaced) and in the second case I cannot even
place HEB correctly as some atoms rearrange after refinement
(heb_wierd.png) and two hydrogens are connected when I add it from the
library (heb_withoutrefine.png)
Thanks, Vera
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Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
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