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 And Paul Emsley has written up a guide about it... 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> on behalf of Gerlind Sulzenbacher <gerlind.sulzenbac...@univ-amu.fr> Sent: Thursday, June 3, 2021 7:10:12 PM To: CCP4BB@JISCMAIL.AC.UK <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 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=C80B0ezyZ5AAWTgXEeVuLEfSw1QljocDI3Kzz6L9vxU%3D&reserved=0 This message was issued to members of https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ZatbCRXPwhVtvLeYyn%2FHMGFGlYKDG5EzQtytvaorIgg%3D&reserved=0, a mailing list hosted by https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KSTwQ%2F9mP4RLd9jwpI%2BvaXya4c%2B5C4Ypdt5FJTM1c%2FU%3D&reserved=0, terms & conditions are available at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2jM32DWn880BnlTvTcyx4DuyEIZ%2BvU1LTEuY4oEksg8%3D&reserved=0 The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT ######################################################################## 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/
