Hi Michel,

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

Chemical Description
Name    5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
Formula C12 H11 N3
Formal charge   0
Molecular weight        197.236 g/mol
Component type  NON-POLYMER


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 
refinement.

Colin


[cid:3A59087A-E871-4A15-8C7F-384F6788170E@man.ac.uk]



Dr. Colin W. Levy
MIB G016
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk<mailto:c.l...@manchester.ac.uk>

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

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On 5 Mar 2018, at 12:30, M T <michel...@gmail.com<mailto:michel...@gmail.com>> 
wrote:

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: 
cif_dictionary_file_selector_create_molecule_checkbutton 
/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.

Michel


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