PS: If you have two different home-brewn ligands, you have to rename one of 
them (pdb and cif), otherwise the same dictionary will be applied to two 
different ligands. Also make sure your cif file is a dictionary and not just a 
coordinate file.

Von: Schreuder, Herman /DE
Gesendet: Montag, 5. März 2018 14:31
Betreff: AW: [ccp4bb] Small molecule not refined in coot.

Hi Colin and Michel,

In my experience, both refmac and coot will use the most recently read-in cif 
dictionary and there is no need to try to find an unique identifier for each 
new ligand one uses. The new dictionary overrides the old one. Finding a unique 
identifier for each new ligand would be a terrible and unnecessary hassle.

What usually goes wrong is that the name of the residue in the pdb file does 
not match the name of the residue in the cif file. And the same holds for the 
atom names. I would check with an editor that the resdue and atom names of the 
pdb file do match the residue and atom names in the cif dictionary.


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Colin 
Gesendet: Montag, 5. März 2018 13:38
Betreff: [EXTERNAL] Re: [ccp4bb] Small molecule not refined in coot.

Hi Michel,

If your ligand is designated as DRG in your pdb then refinement programs will 
anticipate that it is:

Chemical Description



C12 H11 N3

Formal charge


Molecular weight

197.236 g/mol

Component type


If this is not the case then you need to choose a unique identifier, this 
should then allow your cif library to be utilised appropriately during 



Dr. Colin W. Levy
MIB G016
Tel.  0161 275 5090
Mob.07786 197 554<>

 Manchester Institute of Biotechnology | University of Manchester | 3.020 
Garside Building | 131 Princess Street | Manchester | M1 7DN



On 5 Mar 2018, at 12:30, M T <<>> 

Dear all,
I am actually dealing with a structure containing an unnatural ligand.
I generated the pdb file by drawing it on PRODRG server, I did a manual pre-fit 
in the map using coot and I manually merged the pdf file of my protein with the 
one of the ligand.
After that I did few cycles of refinement using Refmac5, with my mtz, my merged 
pdb file and the cif library of the ligand as input files.
First I saw that even if Refmac "completed succesfully" it didn't modify 
coordinates of the ligand, second I saw a warning about the "DRG" molecule in 
the log of Refmac (WARNING: duplicated name of monomer DRG Last entry will be 
used.), third in Coot I cannot use "Real Space Refine Zone" with the ligand and 
when I try to import the CIF dictionary produced by PRODRG (through the server 
or even the one generated through CCP4 ProDrg), it causes Coot crash (** 
(coot-bin:4467): WARNING **: Widget not found: 
/programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288:  4467 Segmentation 
fault: 11  $coot_bin "$@").
Clearly I am not a skilled user of all these programs, so I certainly did 
a/some mistake/s, but if someone can give me tips to be able to refine my 
ligand... Should I rename my DRG molecule, should I verify particular things, 
should I use other ways to generate the pdb and the library of my ligand?
Thank you.

P.S.: I am running CCP4 and coot using SBGRID on a Mac.

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