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: 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]> 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 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/
