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There are lots of GLUCOSE type lib files for different sugars. One way to find what is available is: From the REfinement GUI click Monomer library sketcher You get a window with File in the top LH corner Click on that and ask for Read monomer from library Then enter a key word GLUCOSE and you get this list ADQ etc etc Select what you want and go from there.. Or do this crude method to get a complete list!: [ccp4@roo timm]$ grep -i glucose $CLIBD/monomers/*/* /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/a/ADQ.cif:ADQ ADQ 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE ' non-polymer 61 38 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/a/AGL.cif:AGL AGL '4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE ' pyranose 24 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/b/BG6.cif:BG6 BG6 'BETA-D-GLUCOSE-6-PHOSPHATE ' non-polymer 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/b/BGC.cif:BGC BGC 'BETA-D-GLUCOSE ' pyranose 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/d/D6G.cif:D6G D6G '2-DEOXY-GLUCOSE-6-PHOSPHATE ' pyranose 26 15 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/d/DDA.cif:DDA DDA '2,6-DIDEOXY-BETA-D-GLUCOSE ' pyranose 22 10 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G16.cif:G16 G16 'ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE ' pyranose 30 20 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G1P.cif:G1P G1P 'ALPHA-D-GLUCOSE-1-PHOSPHATE ' pyranose 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G2F.cif:G2F G2F '2-DEOXY-2FLUORO-GLUCOSE ' pyranose 23 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G4D.cif:G4D G4D '4-DEOXY-ALPHA-D-GLUCOSE ' pyranose 23 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6D.cif:G6D G6D '6-DEOXY-ALPHA-D-GLUCOSE ' non-polymer 23 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6P.cif:G6P G6P 'ALPHA-D-GLUCOSE-6-PHOSPHATE ' pyranose 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6Q.cif:G6Q G6Q 'GLUCOSE-6-PHOSPHATE ' non-polymer 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GDA.cif:GDA GDA '4-DEOXY-4-AMINO-BETA-D-GLUCOSE ' non-polymer 25 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GFP.cif:GFP GFP '2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE-1-P' pyranose 26 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLC-B-D.cif:GLC-b-D GLC 'beta_D_glucose ' D-pyranose 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLC.cif:GLC GLC 'ALPHA-D-GLUCOSE ' pyranose 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLD.cif:GLD GLD '4,6-DIDEOXYGLUCOSE ' pyranose 22 10 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLF.cif:GLF GLF '1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE ' pyranose 23 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLO.cif:GLO GLO 'D-GLUCOSE IN LINEAR FORM ' non-polymer 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLT.cif:GLT GLT '5-DEOXY-5-THIO-ALPHA-D-GLUCOSE ' non-polymer 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GMM.cif:GMM GMM 'GLUCOSE MONOMYCOLATE ' non-polymer 200 74 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GUD.cif:GUD GUD 'GLUCOSE-URIDINE-C1,5'-DIPHOSPHATE ' non-polymer 58 36 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/i/ISX.cif:ISX ISX 'GLUCOSE BETA-1,3-ISOFAGAMINE ' non-polymer 44 21 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/k/KBG.cif:KBG KBG '2-KETO-BETA-D-GLUCOSE ' non-polymer 22 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:ADQ ADQ 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE ' non-polymer 61 38 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:AGL AGL '4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE ' pyranose 24 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:BG6 BG6 'BETA-D-GLUCOSE-6-PHOSPHATE ' non-polymer 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:BGC BGC 'BETA-D-GLUCOSE ' pyranose 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:D6G D6G '2-DEOXY-GLUCOSE-6-PHOSPHATE ' pyranose 26 15 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:DDA DDA '2,6-DIDEOXY-BETA-D-GLUCOSE ' pyranose 22 10 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:G16 G16 'ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE ' pyranose 30 20 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:G1P G1P 'ALPHA-D-GLUCOSE-1-PHOSPHATE ' pyranose 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:G2F G2F '2-DEOXY-2FLUORO-GLUCOSE ' pyranose 23 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:G4D G4D '4-DEOXY-ALPHA-D-GLUCOSE ' pyranose 23 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:G6D G6D '6-DEOXY-ALPHA-D-GLUCOSE ' non-polymer 23 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:G6P G6P 'ALPHA-D-GLUCOSE-6-PHOSPHATE ' pyranose 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:G6Q G6Q 'GLUCOSE-6-PHOSPHATE ' non-polymer 27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GDA GDA '4-DEOXY-4-AMINO-BETA-D-GLUCOSE ' non-polymer 25 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GFP GFP '2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE-1-P' pyranose 26 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GLC GLC 'ALPHA-D-GLUCOSE ' pyranose 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GLD GLD '4,6-DIDEOXYGLUCOSE ' pyranose 22 10 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GLF GLF '1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE ' pyranose 23 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GLO GLO 'D-GLUCOSE IN LINEAR FORM ' non-polymer 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GLT GLT '5-DEOXY-5-THIO-ALPHA-D-GLUCOSE ' non-polymer 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GMM GMM 'GLUCOSE MONOMYCOLATE ' non-polymer 200 74 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GUD GUD 'GLUCOSE-URIDINE-C1,5'-DIPHOSPHATE ' non-polymer 58 36 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:ISX ISX 'GLUCOSE BETA-1,3-ISOFAGAMINE ' non-polymer 44 21 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:KBG KBG '2-KETO-BETA-D-GLUCOSE ' non-polymer 22 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:MGL MGL 'O1-METHYL-GLUCOSE ' pyranose 27 13 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:MUG MUG '4-METHYLUMBELLIFERYL-ALPHA-D-GLUCOSE' non-polymer 42 24 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:GLC-b-D GLC 'beta_D_glucose ' pyranose 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:OPG OPG 'OXIRANPSEUDOGLUCOSE ' non-polymer 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:TOA TOA '3-DEOXY-3-AMINO GLUCOSE ' pyranose 26 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:TOC TOC '2,3,6-TRIDEOXY-2,6-DIAMINO GLUCOSE ' pyranose 27 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:UPG UPG 'URIDINE-5'-DIPHOSPHATE-GLUCOSE ' non-polymer 58 36 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:VG1 VG1 'ALPHA-D-GLUCOSE-1-PHOSPHATE-6-VANADA' pyranose 31 20 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif: NAG-b-L NAG-b-D SUG-b-L beta_L_N-acetyl-Glucose L-pyranose /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif: GLC-b-L GLC-b-D SUG-b-L beta_L_glucose L-pyranose /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif: NAG-a-D NAG-b-D SUG-a-D alpha_D_N-acetyl-Glucose D-pyranose /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif: GLC-a-D GLC-b-D SUG-a-D alpha_D_glucose D-pyranose /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif: NAG-a-L NAG-b-D SUG-a-L alpha_L_N-acetyl-Glucose L-pyranose /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif: GLC-a-L GLC-b-D SUG-a-L alpha_L_glucose L-pyranose /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/m/MGL.cif:MGL MGL 'O1-METHYL-GLUCOSE ' pyranose 27 13 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/m/MUG.cif:MUG MUG '4-METHYLUMBELLIFERYL-ALPHA-D-GLUCOSE' non-polymer 42 24 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/o/OPG.cif:OPG OPG 'OXIRANPSEUDOGLUCOSE ' non-polymer 24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/t/TOA.cif:TOA TOA '3-DEOXY-3-AMINO GLUCOSE ' pyranose 26 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/t/TOC.cif:TOC TOC '2,3,6-TRIDEOXY-2,6-DIAMINO GLUCOSE ' pyranose 27 11 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/u/UPG.cif:UPG UPG 'URIDINE-5'-DIPHOSPHATE-GLUCOSE ' non-polymer 58 36 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/v/VG1.cif:VG1 VG1 'ALPHA-D-GLUCOSE-1-PHOSPHATE-6-VANADA' pyranose 31 20 . On 5 March 2014 15:23, Remie Fawaz-Touma <[log in to unmask]> wrote: > > > Hi, > > I am trying to refine (Refmac5 on CCP4) a protein structure containing > ligands that are exclusively glucose units but refinement fails because I > don't have a lib file for the sugars. Can I get help on making lib files > please? > > Thank you, > > Remie > > >