[phenixbb] GeoStd: was definition of glycosylation in phenix.refine

Tue Nov 18 14:57:55 PST 2014

Hi Nigel,

could you please comment on any plans to harmonize the use of these restraints for other refinement programs as well. Phenix originally appears to have implemented the restraint dictionaries from CCP4. Right now there seems to be some kind of parallel development going on with the dictionaries being in sync to some degree. Is there a plan to move to a unified restraints distribution at some point?

Thanks

                Carsten

From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Nigel Moriarty
Sent: Tuesday, November 18, 2014 12:38 PM
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] definition of glycosylation in phenix.refine

@Laurent

Engin advice is sound but you are having trouble free feel to send me the inputs directly.

NB. Any files sent to me will be held in strictest confidence.

@Engin

I think you will find what you are looking for in the GeoStd. As restraints are improved, they are moved from $PHENIX/chem_data/mon_lib to $PHENIX/chem_data/geostd (which is hosted on SourceForge for anybody's use). The directory structure is the same as the Monomer Library with a geostd_list.cif file corresponding to mon_lib_list.cif which specifies the links.

Cheers

Nigel

---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov<mailto:NWMoriarty at LBL.gov>
Fax   : 510-486-5909       Web  : CCI.LBL.gov<http://CCI.LBL.gov>

On Tue, Nov 18, 2014 at 8:25 AM, Engin Özkan <eozkan at uchicago.edu<mailto:eozkan at uchicago.edu>> wrote:
Hi Laurent,

If I am reading the error message right, you did not delete the hydrogens that get removed upon bond formation. That's what it is complaining about. I always thought Phenix probably removed these atoms (the hydroxyl and the hydrogen) automatically when you defined the link, but never tested if it really does it.

I also usually remove all hydrogens right away when sugar residues are inserted.

Finally, I will recommend that you use automatic linking in the phenix.refine GUI. It works great (I am on the latest nightly, dev-1839; you may need to upgrade). No need to define pesky links anymore. Thank you developers!

At the risk of hijacking the thread, I could not find in my installation the cif files for N-linked sugars. Have they been moved elsewhere?

Hope this helps,
Engin

On 11/18/14 10:02 AM, Laurent Maveyraud wrote:
Hi,

I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links...
The glycosylatin is
Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064

This is what I add in the eff file :
apply_cif_link {
  data_link = NAG-ASN
  residue_selection_1 = chain D and resname NAG and resid 1061
  residue_selection_2 = chain A and resname ASN and resid 638
}
apply_cif_link {
  data_link = BETA1-4
  residue_selection_1 = chain D and resname NAG and resid 1062
  residue_selection_2 = chain D and resname NAG and resid 1061
}
apply_cif_link {
  data_link = BETA1-4
  residue_selection_1 = chain D and resname BMA and resid 1063
  residue_selection_2 = chain D and resname NAG and resid 1062
}
apply_cif_link {
  data_link = ALPHA1-3
  residue_selection_1 = chain D and resname MAN and resid 1064
  residue_selection_2 = chain D and resname BMA and resid 1063
}
this is correctly read in refine:
  apply_cif_link:
    data_link: NAG-ASN
      mod_id_1: DEL-O1
      mod_id_2: DEL-HD22
    residue_selection_1: chain D and resname NAG and resid 1061
    residue_selection_2: chain A and resname ASN and resid 638
  apply_cif_link:
    data_link: BETA1-4
      mod_id_1: DEL-HO4
      mod_id_2: DEL-O1
    residue_selection_1: chain D and resname NAG and resid 1062
    residue_selection_2: chain D and resname NAG and resid 1061
  apply_cif_link:
    data_link: BETA1-4
      mod_id_1: DEL-HO4
      mod_id_2: DEL-O1
    residue_selection_1: chain D and resname BMA and resid 1063
    residue_selection_2: chain D and resname NAG and resid 1062
  apply_cif_link:
    data_link: ALPHA1-3
      mod_id_1: DEL-HO3
      mod_id_2: DEL-O1
    residue_selection_1: chain D and resname MAN and resid 1064
    residue_selection_2: chain D and resname BMA and resid 1063
but generates an error :

  Number of atoms with unknown nonbonded energy type symbols: 5
    "HETATM10951  HO4 NAG D1052 .*.     H  "
    "HETATM10973  HO4 BMA D1053 .*.     H  "
    "HETATM11028  HO4 NAG D1062 .*.     H  "
    "HETATM11050  HO4 BMA D1063 .*.     H  "
    "HETATM11070  HO3 MAN D1064 .*.     H  "

and the job stops.

Any ideas on what if wrong ?

thanks for your help

Laurent

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