Re: [ccp4bb] CCP4 lib file
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-polymer61 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-polymer27 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-polymer23 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-polymer27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GDA.cif:GDA GDA '4-DEOXY-4-AMINO-BETA-D-GLUCOSE ' non-polymer25 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-polymer24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLT.cif:GLT GLT '5-DEOXY-5-THIO-ALPHA-D-GLUCOSE ' non-polymer24 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-polymer58 36 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/i/ISX.cif:ISX ISX 'GLUCOSE BETA-1,3-ISOFAGAMINE' non-polymer44 21 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/k/KBG.cif:KBG KBG '2-KETO-BETA-D-GLUCOSE ' non-polymer22 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:ADQ ADQ 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE' non-polymer61 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-polymer27 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
Re: [ccp4bb] CCP4 lib file
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-polymer61 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-polymer27 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-polymer23 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-polymer27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GDA.cif:GDA GDA '4-DEOXY-4-AMINO-BETA-D-GLUCOSE ' non-polymer25 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-polymer24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLT.cif:GLT GLT '5-DEOXY-5-THIO-ALPHA-D-GLUCOSE ' non-polymer24 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-polymer58 36 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/i/ISX.cif:ISX ISX 'GLUCOSE BETA-1,3-ISOFAGAMINE' non-polymer44 21 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/k/KBG.cif:KBG KBG '2-KETO-BETA-D-GLUCOSE ' non-polymer22 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:ADQ ADQ 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE' non-polymer61 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-polymer27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:BGC BGC 'BETA-D-GLUCOSE
Re: [ccp4bb] CCP4 lib file
On 07/03/14 11:51, Remie wrote: I ended up using a glucose ligand lib file from a different protein that my friend used and refinement Refmac5 worked out. The mind boggles :)... well, OK. However I need to add the LINK Command in PDB so CCP4 recognizes that glucoses connected. In Coot, at least: Extensions - Modelling - Make a Link [click, click] Paul.
[ccp4bb] CCP4 lib file
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
Re: [ccp4bb] CCP4 lib file
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-polymer61 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-polymer27 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-polymer23 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-polymer27 16 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GDA.cif:GDA GDA '4-DEOXY-4-AMINO-BETA-D-GLUCOSE ' non-polymer25 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-polymer24 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLT.cif:GLT GLT '5-DEOXY-5-THIO-ALPHA-D-GLUCOSE ' non-polymer24 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-polymer58 36 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/i/ISX.cif:ISX ISX 'GLUCOSE BETA-1,3-ISOFAGAMINE' non-polymer44 21 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/k/KBG.cif:KBG KBG '2-KETO-BETA-D-GLUCOSE ' non-polymer22 12 . /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:ADQ ADQ 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE' non-polymer61 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-polymer27 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 .
