Hi Don and Vera,
Coot will handle the ligand properly without "pre-integrating" it into the PDB.
Read the ligand (if it's not in the monomer library already) into aceDRG (in
any form that it accepts), then in Coot, read the generated cif file -> get
monomer (when positioned in the correct place)- > make link (click the atoms
you want to link) and that's it. I would start only with the covalent link to
the iron and leave the potential links to the propionates for later, just to
see how it works.
This is all working within the Refmac environments. As for Phenix, there has
been a recent discussion on the issue. I'm sure Phenix people would guide
through the necessary steps to get the Coot-Phenix combination to work.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dom Bellini -
MRC LMB <dbell...@mrc-lmb.cam.ac.uk>
Sent: Tuesday, July 13, 2021 5:15 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Problems with refining covalently linked heme cofactor
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
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839
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