[phenixbb] Glycan refinement

Mooers, Blaine H.M. (HSC) Blaine-Mooers at ouhsc.edu
Tue Nov 10 11:23:03 PST 2009

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 \

Best regards,


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:  blaine-mooers at ouhsc.edu

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [tzhou at mail.nih.gov]
Sent: Tuesday, November 10, 2009 12:12 PM
To: 'phenixbb at phenix-online.org'
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.



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.

More information about the phenixbb mailing list