[phenixbb] Glycan refinement

[Mooers, Blaine H.M. (HSC)]

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

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________________________________________
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.

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)
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