Dear Gerlind, I'm glad that we were of help! I should point out that the "Make link (click 2 atoms)" is dangerous as it only generates a LINK record but not a full link dictionary - it should only be used for common known links that are present in the monomer library. This issue is discussed in section 4.4 of the article I posted earlier (https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html). I'd ignore Coot's "Make link" tool unless you really know what you're doing. Otherwise, I'd favour the AceDRG interfaces as recommended in that article.
Regards, Rob > On 3 Jun 2021, at 20:13, Gerlind Sulzenbacher > <gerlind.sulzenbac...@univ-amu.fr> wrote: > > Dear David and Rob, > > thanks a lot for your help and your suggestions. > Following your suggestions I found in Coot the very neat solution "Make link > (click 2 atoms ...): Much better than my previous dinosaur approach. > Thanks again and all the best, > Gerlind > > > On 03/06/2021 20:17, David Briggs wrote: >> Hi Gerlind, >> >> Rob Nicholls gave a talk on how to deal with covalent linkages using AceDrg >> at CCP4 study weekend in 2020. >> >> https://youtu.be/p4oTJ0bjD3M <https://youtu.be/p4oTJ0bjD3M> >> >> And Paul Emsley has written up a guide about it... >> >> https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html >> <https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html> >> >> Hopefully these will be useful for you. >> >> Good luck, >> >> Dave >> >> -- >> Dr David C. Briggs >> Senior Laboratory Research Scientist >> Signalling and Structural Biology Lab >> The Francis Crick Institute >> London, UK >> == >> about.me/david_briggs >> >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> >> <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Gerlind Sulzenbacher >> <gerlind.sulzenbac...@univ-amu.fr> <mailto:gerlind.sulzenbac...@univ-amu.fr> >> Sent: Thursday, June 3, 2021 7:10:12 PM >> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> >> <CCP4BB@JISCMAIL.AC.UK> <mailto:CCP4BB@JISCMAIL.AC.UK> >> Subject: [ccp4bb] help needed with link description >> >> >> External Sender: Use caution. >> >> >> 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 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