Thanks a lot Paul for the quick reply,
Just in case I validate FLEV was working properly using the 1a4m structure
(loaded as a .cif file from the PDB). Indeed once I hydrogenate the region, I
see all the h-bonds.
Now I’ve tried to do that on my own files … still can’t get it to work
* From buster refine > Pdb file containing ligand > import cif
dictionnaries (include hydrogens) > hydrogenate region > no Hbonds appear.
* From buster refine > model.cif file containing ligand > import cif
dictionnaries (include hydrogens) > hydrogenate region > no Hbonds appear
Interestingly on the 1a4m I don’t need to load restraints (which is normal with
the mmcif format), but on the mmcif format generated by buster I still have to
load restraint separately to toggle FLEV.
“From BUSTER
The two relevant files for deposition of BUSTER refinement results are
* BUSTER_model.cif: This file contains the atomic model as well as any
non-standard restraint information (e.g. for a unique ligand or compound).
* It also contains the refinement statistics (R values, number of
reflections used etc). »
Can it be a formatting issue ?
Thanks in advance for your help
/Xavier
De : Paul Emsley <[email protected]>
Envoyé : mercredi 4 février 2026 10:13
À : Xavier KUBIAK <[email protected]>; [email protected]
Objet : [EXTERNAL] - Re: FLEV Coot 0.9 H-bonds and water molecules not shown
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On 04/02/2026 07:44, Xavier KUBIAK wrote:
Dear community,
Hello Xavier,
I’m using Coot 0.9 to generate ligand plots with FLEV.
I’m having trouble with 2 things :
* Showing hydrogen bonds with the surrounding residues : the ones shown
with the Environement distance do not pop in the FELV view
* Showing the water molecules (weither they have the same chain ID as the
ligand/protein or not)
I “Toggle FLEV interactions for this residues” then “FLEV this residues”.
I have the same issue with Coot1.14 (I’ve asked to have the latest version
installed).
The documentation for FLEV is not very good.
1: you need to add hydrogen atoms to the model for Coot to find hydrogen bonds
2: the was a bug in previous versions where some hydrogen bonds might have been
missed (thanks to Lan Guan for bringing this to my attention). This was fixed
in 1.1.20.
I've tried to make the distribution of Coot so that you don't need to be admin
to install it.
Paul.
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