Actually, the situation is more complex. If I use 4fxk downloaded straight from the PDB, the parser in phenix.link_edits fails to find the LINK records, leading to phenix.ready_set incorrectly adding hydrogens. If, however, I take the same file and strip it back to the bare minimum (CRYST, LINK and ATOM cards) it works fine. Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email. On 27 Apr 2015, at 7:01 pm, Luca Jovine mailto:[email protected]> wrote: Yes, I also saw this... a solution is to manually edit the PDB file output by phenix.read_set to get rid of HD22 of N-linked Asn residues - then phenix.refine works. HTH, Luca ------------------------------------------------------------------------ Luca Jovine, Ph.D. Professor of Structural Biology & EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition & Center for Innovative Medicine Halsovagen 7, SE-141 83 Huddinge, Sweden Voice: +46.(0)8.524-81136 FAX: +46.(0)8.6081-501 E-mail: [email protected]mailto:[email protected] W3: http://jovinelab.org ------------------------------------------------------------------------ On 27 Apr 2015, at 10:52, Tristan Croll mailto:[email protected]> wrote: Hi, I'm currently using the dev 2000 version of Phenix, and noticed an issue with the automatic linking of N-linked (and presumably O-linked) glycans. If you feed a glycosylated structure sans hydrogens to Phenix and allow ReadySet to add hydrogens prior to refinement, it adds hydrogens as if the glycans are unlinked. Then, the automatic linking script rejects them due to valence issues. Cheers, Tristan _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]