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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Nigel,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> Carsten<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Nigel Moriarty<br>
<b>Sent:</b> Tuesday, November 18, 2014 12:38 PM<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] definition of glycosylation in phenix.refine<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">@Laurent<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Engin advice is sound but you are having trouble free feel to send me the inputs directly.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">NB. Any files sent to me will be held in strictest confidence.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">@Engin<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<p class="MsoNormal">Cheers<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Nigel<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">---<o:p></o:p></p>
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<p class="MsoNormal">Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, Nov 18, 2014 at 8:25 AM, Engin Özkan <<a href="mailto:eozkan@uchicago.edu" target="_blank">eozkan@uchicago.edu</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">Hi Laurent,<br>
<br>
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.<br>
<br>
I also usually remove all hydrogens right away when sugar residues are inserted.<br>
<br>
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!<br>
<br>
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?<br>
<br>
Hope this helps,<br>
Engin<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
On 11/18/14 10:02 AM, Laurent Maveyraud wrote:<o:p></o:p></p>
<p class="MsoNormal">Hi,<br>
<br>
I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links...<br>
The glycosylatin is<br>
Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064<br>
<br>
This is what I add in the eff file :<br>
apply_cif_link {<br>
data_link = NAG-ASN<br>
residue_selection_1 = chain D and resname NAG and resid 1061<br>
residue_selection_2 = chain A and resname ASN and resid 638<br>
}<br>
apply_cif_link {<br>
data_link = BETA1-4<br>
residue_selection_1 = chain D and resname NAG and resid 1062<br>
residue_selection_2 = chain D and resname NAG and resid 1061<br>
}<br>
apply_cif_link {<br>
data_link = BETA1-4<br>
residue_selection_1 = chain D and resname BMA and resid 1063<br>
residue_selection_2 = chain D and resname NAG and resid 1062<br>
}<br>
apply_cif_link {<br>
data_link = ALPHA1-3<br>
residue_selection_1 = chain D and resname MAN and resid 1064<br>
residue_selection_2 = chain D and resname BMA and resid 1063<br>
}<br>
this is correctly read in refine:<br>
apply_cif_link:<br>
data_link: NAG-ASN<br>
mod_id_1: DEL-O1<br>
mod_id_2: DEL-HD22<br>
residue_selection_1: chain D and resname NAG and resid 1061<br>
residue_selection_2: chain A and resname ASN and resid 638<br>
apply_cif_link:<br>
data_link: BETA1-4<br>
mod_id_1: DEL-HO4<br>
mod_id_2: DEL-O1<br>
residue_selection_1: chain D and resname NAG and resid 1062<br>
residue_selection_2: chain D and resname NAG and resid 1061<br>
apply_cif_link:<br>
data_link: BETA1-4<br>
mod_id_1: DEL-HO4<br>
mod_id_2: DEL-O1<br>
residue_selection_1: chain D and resname BMA and resid 1063<br>
residue_selection_2: chain D and resname NAG and resid 1062<br>
apply_cif_link:<br>
data_link: ALPHA1-3<br>
mod_id_1: DEL-HO3<br>
mod_id_2: DEL-O1<br>
residue_selection_1: chain D and resname MAN and resid 1064<br>
residue_selection_2: chain D and resname BMA and resid 1063<br>
but generates an error :<br>
<br>
Number of atoms with unknown nonbonded energy type symbols: 5<br>
"HETATM10951 HO4 NAG D1052 .*. H "<br>
"HETATM10973 HO4 BMA D1053 .*. H "<br>
"HETATM11028 HO4 NAG D1062 .*. H "<br>
"HETATM11050 HO4 BMA D1063 .*. H "<br>
"HETATM11070 HO3 MAN D1064 .*. H "<br>
<br>
and the job stops.<br>
<br>
Any ideas on what if wrong ?<br>
<br>
thanks for your help<br>
<br>
Laurent<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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