[phenixbb] GeoStd: was definition of glycosylation in phenix.refine
Schubert, Carsten [JRDUS]
CSCHUBER at its.jnj.com
Tue Nov 18 14:57:55 PST 2014
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?
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
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.
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.
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:
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,
On 11/18/14 10:02 AM, Laurent Maveyraud wrote:
I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links...
The glycosylatin is
This is what I add in the eff file :
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
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
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
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:
residue_selection_1: chain D and resname NAG and resid 1061
residue_selection_2: chain A and resname ASN and resid 638
residue_selection_1: chain D and resname NAG and resid 1062
residue_selection_2: chain D and resname NAG and resid 1061
residue_selection_1: chain D and resname BMA and resid 1063
residue_selection_2: chain D and resname NAG and resid 1062
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
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