If your ligand is not in the monomer library and it is generated via AceDRG or
grade, you need to import the CIF dictionary:
In the script change chapi.get_monomer() with this:
imol_enc = chapi.get_imol_enc_any()
chapi.import_cif_dictionary("LIG.cif", imol_enc)
And make sure the LIG.cif is in the same directory where you run the script.
In case you still have problems, send me an email and we will try to figure it
out.
Lucrezia
> On 12 Feb 2026, at 11:08, Xavier KUBIAK <[email protected]> wrote:
>
> CAUTION: This email originated from outside of the LMB:
> [email protected] <mailto:[email protected]>-.
> Do not click links or open attachments unless you recognize the sender and
> know the content is safe.
> If you think this is a phishing email, please forward it to
> [email protected] <mailto:[email protected]>
>
> --
>
> Hi all,
>
> Unfortunately @Lucrezia Catapano <mailto:[email protected]>, I could
> not make your solution work.
>
> I think I am narrowing down the problem but can’t figure out a solution.
>
> My protein contains 2 ligands (one internal, and one from the ccp4 library) :
> in the same PDB file, FLEV works perfectly fine with the ccp4 library one,
> but not with my own ligand. I’ve tried the following :
> Generate the LIG.cif file with both aceDRG and Grade2 > no H bonds
> Change to occupancy of Hydrogens to 1.0 on my ligand (by defaut they are set
> to 0) > no H bonds
> In both cases, no water is detected around the LIG.cif but properly around
> the cco4 library ligand.
> Any thoughts ?
>
> Best
> /Xavier
>
> De : Mailing list for users of COOT Crystallographic Software
> <[email protected] <mailto:[email protected]>> De la part de Xavier KUBIAK
> Envoyé : mercredi 11 février 2026 14:09
> À : [email protected] <mailto:[email protected]>
> Objet : [EXTERNAL] - Re: [EXTERNAL] - Re: [EXTERNAL] - Re: [EXTERNAL] - Re:
> FLEV Coot 0.9 H-bonds and water molecules not shown
>
>
>
> *** [EXTERNAL] This message comes from an external organization. Exercise
> caution when opening attachments or clicking links, especially from unknown
> senders. ***
> Thanks @Lucrezia Catapano <mailto:[email protected]> for the very
> useful info and the link, I’ll try that.
>
> Best
> /Xavier
>
> De : Lucrezia Catapano <[email protected]
> <mailto:[email protected]>>
> Envoyé : mercredi 11 février 2026 11:15
> À : Xavier KUBIAK <[email protected] <mailto:[email protected]>>
> Cc : [email protected] <mailto:[email protected]>
> Objet : [EXTERNAL] - Re: [EXTERNAL] - Re: [EXTERNAL] - Re: FLEV Coot 0.9
> H-bonds and water molecules not shown
>
>
>
> *** [EXTERNAL] This message comes from an external organization. Exercise
> caution when opening attachments or clicking links, especially from unknown
> senders. ***
> For your information, FLEV can be generated using the Python chapi library,
> which is part of Coot and is available via ccp4-python and Conda.
>
> There is a script example in the documentation webpage:
> mrc-lmb.cam.ac.uk
> <https://www.mrc-lmb.cam.ac.uk/lucrezia/libcootapi-documentation/read_coordinates.html#id4>
>
> <image001.png>
> <https://www.mrc-lmb.cam.ac.uk/lucrezia/libcootapi-documentation/read_coordinates.html#id4>
>
>
> Lucrezia
>
> Lucrezia Catapano, PhD (she/her)
> Postdoctoral Scientist
> Murshudov Group
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Biomedical Campus, Cambridge CB2 0QH, UK.
>
>
>
>
> On 11 Feb 2026, at 09:20, Xavier KUBIAK
> <[email protected]
> <mailto:[email protected]>> wrote:
>
> CAUTION: This email originated from outside of the LMB:
> [email protected] <mailto:[email protected]>-.
> Do not click links or open attachments unless you recognize the sender and
> know the content is safe.
> If you think this is a phishing email, please forward it to
> [email protected] <mailto:[email protected]>
>
> --
>
> Dear community,
>
> I am still stuck with my (probably) basic FLEV issue below, could someone be
> of help ?
> Thanks again for your time.
> All the best
> /Xavier
>
> De : Mailing list for users of COOT Crystallographic Software
> <[email protected] <mailto:[email protected]>> De la part de Xavier KUBIAK
> Envoyé : mercredi 4 février 2026 18:07
> À : [email protected] <mailto:[email protected]>
> Objet : [EXTERNAL] - Re: [EXTERNAL] - Re: FLEV Coot 0.9 H-bonds and water
> molecules not shown
>
>
>
> *** [EXTERNAL] This message comes from an external organization. Exercise
> caution when opening attachments or clicking links, especially from unknown
> senders. ***
> 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]
> <mailto:[email protected]>>
> Envoyé : mercredi 4 février 2026 10:13
> À : Xavier KUBIAK <[email protected] <mailto:[email protected]>>;
> [email protected] <mailto:[email protected]>
> Objet : [EXTERNAL] - Re: FLEV Coot 0.9 H-bonds and water molecules not shown
>
>
>
> *** [EXTERNAL] This message comes from an external organization. Exercise
> caution when opening attachments or clicking links, especially from unknown
> senders. ***
> 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.
>
>
>
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>
>
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>
########################################################################
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
