[phenixbb] Glycan refinement

[Engin Ozkan]

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
>
> 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
> http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
>
> ________________________________________
> 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)
> ******************************************************************
> 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.
> ******************************************************************
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>    


-- 
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111