Dear Phenix developers, I am solving a protein-dna complex and Autobuild is able to build both the protein as well as DNA chain (one at a time). However, when I try to do the refinement, I get an error saying "Phenix could not find the geometry restraints in the standard monomer library for one or more residues in the pdb file... DG: 6 copies, DA: 3 copies, DT: 43 copies". It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this. Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA and doesn't like the above phenix style. In order to manipulate in coot, I had to rename all the bases...is it possible to have a format that is compatible both in Phenix and Coot or am I missing something obvious here. Thanks and Have a great weekend! Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.