Hello, I get this same error sometimes when I mutate a DNA base. For some reason, Coot will sometimes add an extra atom – not necessarily attached to the base. To correct the error you must find and delete the atom. You can look for it in the Coot interface or you can manually delete it from the text of the pdb file. If you manually remove it, you will need to correct the numbering, and this website will be helpful:
http://www.canoz.com/sdh/renumberpdbatoms.pl Good luck, Rachel Werther From: Mailing list for users of COOT Crystallographic Software <[email protected]<mailto:[email protected]>> on behalf of Xiao Lei <[email protected]<mailto:[email protected]>> Reply-To: Xiao Lei <[email protected]<mailto:[email protected]>> Date: Tuesday, October 17, 2017 at 1:04 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Coot fail real space refine of DNA Dear All, I got an error when I do real space refine with DNA base in Coot, Refmac5 did not give me any error, however Coot give the error as attach. I do not know how to fix this.
