Have you run refmac with the Review restraints option - that generates LINKs if they seem necessary. Or can you use the SUGAR links already set upin the library? Eleanor
On 7 March 2014 11:51, Remie <remiefa...@gmail.com> wrote: > Thanks Eleanor, > I ended up using a glucose ligand lib file from a different protein that > my friend used and refinement Refmac5 worked out. > However I need to add the LINK Command in PDB so CCP4 recognizes that > glucoses connected. > Can I get help please? > Thank you, > Remie > > > On Mar 5, 2014, at 10:49 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > > 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 <remiefa...@gmail.com> 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 >> >> >> >
