[phenixbb] definition of glycosylation in phenix.refine

Nigel Moriarty nwmoriarty at lbl.gov
Tue Nov 18 09:38:01 PST 2014


@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
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Nov 18, 2014 at 8:25 AM, Engin Özkan <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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