Hi Blaine, That might not work correctly. You may get the stereochemistry of the linkage incorrect if you use just a bond distance restraint. You should use linkage types like BETA1-4, or ALPHA1-6, depending on the type of the linkage. And as I have mentioned in the email before, you should also call your beta mannose BMA, and alpha mannose MAN (see the references I mentioned in that email). So something like this would be my guess: apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 902 residue_selection_2 = chain A and resname BMA and resid 903 } apply_cif_link { data_link = ALPHA1-6 residue_selection_1 = chain A and resname BMA and resid 903 residue_selection_2 = chain A and resname MAN and resid 904 } Please correct me if I am wrong. Engin On 11/10/09 11:23 AM, Mooers, Blaine H.M. (HSC) wrote:
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: [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. ******************************************************************
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