Dear Gerlind, Where did you get your mad_monlib.cif file? It shouldn't be neccesary for you to be manually modifying such restraint dictionaries (any more). You can generate these using AceDRG, either via CCP4i2 or Coot.
Shameless plug: https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html https://journals.iucr.org/d/issues/2021/06/00/ir5022/index.html Regards, Rob Dr Rob Nicholls Senior Investigator Scientist MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH > On 3 Jun 2021, at 19:10, Gerlind Sulzenbacher > <gerlind.sulzenbac...@univ-amu.fr> wrote: > > Dear all, > > I am going litteraly mad (or just old). > > I would like to make a covalent link between a carbohydrate moiety and and > ASP of my well-cheered protein. > > The identifier for the carbohydrate moiety is MAD, chain C, res number 1. > > The link is established between C5 of MAD and OD2 of ASP 518, chain A. > > In the mad_monlib.cif I added the following: > > data_link_list > loop_ > _chem_link.id > _chem_link.comp_id_1 > _chem_link.mod_id_1 > _chem_link.group_comp_1 > _chem_link.comp_id_2 > _chem_link.mod_id_2 > _chem_link.group_comp_2 > _chem_link.name > ASP-MAD ASP . . MAD . . > bond_ASP-OD2_=_MAD-C5 > # > data_link_ASP-MAD > # > loop_ > _chem_link_bond.link_id > _chem_link_bond.atom_1_comp_id > _chem_link_bond.atom_id_1 > _chem_link_bond.atom_2_comp_id > _chem_link_bond.atom_id_2 > _chem_link_bond.type > _chem_link_bond.value_dist > _chem_link_bond.value_dist_esd > ASP-MAD 1 OD2 2 C5 . 1.370 0.040 > > In the entry PDB file I added the line: > > LINK OD2 ASP A 518 C5 MAD C 1 > > The log file of REFMAC tells me > > INFO: link is found (not be used) dist= 1.370 ideal_dist= 1.370 > ch:AAA res: 518 ASP at:OD2 .->ch:CCC res: 1 > MAD at:C5 . > > And the expression "not be used" is certainly the case, as the distance of > the covalent bond changes from 1.37 to 1.6 Å. > > The data resolution is 1.8 Å. > > If somebody could please point out what I am doing wrong, I'd be very > grateful. > > With best wishes, > > Gerlind > > > -- > Gerlind Sulzenbacher > Architecture et Fonction des Macromolécules Biologiques > UMR7257 CNRS, Aix-Marseille Université > Case 932 > 163 Avenue de Luminy > 13288 Marseille cedex 9 > France > Tel +33 491 82 55 66 > Fax +33 491 26 67 20 > E-mail: gerlind.sulzenbac...@univ-amu.fr > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
