The protocol for using Coot and Acedrg for links was described by Rob
Nicholls here:
https://www.youtube.com/watch?v=p4oTJ0bjD3M
Things look a bit different in Coot 1 and there was some work done
(about a year ago?) to address linking failures.
Paul.
On 22/11/2025 14:26, Amit Meir wrote:
Hi all,
Can someone please help us out with forming a PTM to a side chain?
We can refine the PTM ligand in its density (as a non-bonded ligand), but the
side chain will not stay within the distant specified on the PDB file.
So far, we tried:
1. Using "make link" in Coot, between the specific atoms (side chain and PTM)
2. Made sure the line is present in the pdb file:
LINK NZ LYS A 630 C11 PTM A 701 1555 1555 1.33
[PTM is an acronym for our specific PTM. I'm keeping it anonymous for now, but
the modification is on a Lys]
3. Generated a PTM.cif file for the ligand using eLbow, and included it in real
time refinement (it's an EM map) in Phenix
We also tried to use Isolde (sorry...) and force "bond sel reasonable false"
followed by an Isolde run. But then Isolde, which could recognize this specific PTM,
insisted on adding extra incorrect hydrogens (ie Lys Nz has *2H* (instead of 1) plus the
connection to CE, plus the connection to the PTM). We manually removed the extra
hydrogens before another round in Phenx, but the bond between the Nz and the PTM still
break the laws of chemistry (we get sharp angles, for example).
We saw people depositing those structures, and it seems fine in theirs
(reasonable bond length and angle)
Can anyone have other suggestions, please?
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