Hi Tongqing, Make a sugars.edits ascii file with links like the following between two manoses refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name O2 and chain A and resname MAN and resseq 1490 atom_selection_2 = name C1 and chain A and resname MAN and resseq 1491 distance_ideal = 1.439000 sigma = 0.020 } } and then include this file when running phenix.refine in the command mode, e.g. phenix.refine --overwrite 715_scala1.mtz 25sugars.pdb 25sugars.edits \ refinement.input.xray_data.labels=IMEAN_XDSdataset,SIGIMEAN_XDSdataset \ strategy=individual_sites+individual_adp simulated_annealing=true \ main.number_of_macro_cycles=10 Best regards, Blaine ********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877 ________________________________________ From: [email protected] [[email protected]] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [[email protected]] Sent: Tuesday, November 10, 2009 12:12 PM To: '[email protected]' Subject: [phenixbb] Glycan refinement Dear All, I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************