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<div class=Section1>
<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 lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Dear All, <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span
lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><span style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'>thank you very much for the
help with the glycosylations. </span><span lang=EN-US style='font-size:10.0pt;
font-family:"Courier New"'>Blaine was right yesterday that I just forgot to set
the last brace. </span><span lang=EN-US style='font-size:11.0pt;font-family:
"Calibri","sans-serif";color:#1F497D'>As this is also a common question, I
thought maybe the “manual” I wrote now for this issue can be put also in the
FAQs .(lots I wrote is just pasted from the manual.<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo4;
text-autospace:none'><![if !supportLists]><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New"'><span style='mso-list:Ignore'>1)<span
style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>check if you take
the right sugars. BMA is not same as MAN for example. good papers are:</span><b><span
lang=EN-US style='font-size:16.0pt;font-family:"GillSans-Bold","sans-serif"'><o:p></o:p></span></b></p>
<p class=MsoListParagraph style='text-autospace:none'><b><span lang=EN-US
style='font-size:16.0pt;font-family:"GillSans-Bold","sans-serif"'> <o:p></o:p></span></b></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-family:"GillSans-Bold","sans-serif"'>pdb-care (PDB CArbohydrate
REsidue check): a program to support annotation of complex carbohydrate
structures in PDB files </span><span lang=EN-US style='font-size:10.0pt;
font-family:"Giovanni-Book","sans-serif"'>Thomas L�tteke and Claus-W von der
Lieth</span><span lang=EN-US style='font-family:"Giovanni-Book","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-family:"AdvPSTim","sans-serif"'>Data mining the protein data bank:
automatic detection and assignment of carbohydrate structures </span><span
lang=EN-US style='font-size:10.0pt;font-family:"AdvPSTim","sans-serif"'>Thomas
L</span><span lang=EN-US style='font-size:10.0pt;font-family:AdvP4C4E59'>�</span><span
lang=EN-US style='font-size:10.0pt;font-family:"AdvPSTim","sans-serif"'>tteke,
Martin Frank and Claus-W. von der Lieth</span><span lang=EN-US
style='font-family:"AdvPSTim","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>2) check which links you
need. There are already lots of predefined links in phenix stored in the
file mon_lib_list.cif<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>The full path to this file
can be obtained with the command:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>%
phenix.where_mon_lib_list_cif<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>All apply_cif_modification and
apply_cif_link definitions will be included into the .def files. I.e. it is not
necessary to specify the definitions again if further refinement runs are
started with .def files. Note that all LINK, SSBOND, HYDBND, SLTBRG and CISPEP
records in the input PDB files are ignored.<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>3) Create a file which you
can call whatever you want even the extension doesn't matter. E.g.:
cif_link.params<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>Put in this file your links:
(Which <u>Atom</u> of residue1 will be connected to which <u>Atom</u> in
residue2 is already defined in mon_lib_list.cif)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>refinement.pdb_interpretation.apply_cif_link
{<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
data_link = NAG-ASN<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_1 = chain A and resname NAG and resid 500<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_2 = chain A and resname ASN and resid 297<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'> }<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
refinement.pdb_interpretation.apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
data_link = BETA1-4<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_1 = chain A and resname NAG and resid 500<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_2 = chain A and resname NAG and resid 501<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'> }<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
refinement.pdb_interpretation.apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
data_link = BETA1-4<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_1 = chain A and resname NAG and resid 501<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_2 = chain A and resname BMA and resid 502<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'> }<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
refinement.pdb_interpretation.apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
data_link = ALPHA1-3.<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_1 = chain A and resname BMA and resid 502<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_2 = chain A and resname MAN and resid 503<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'> }<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>4) run % phenix.refine
model.pdb data.hkl cif_link.params<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>5)Trouble shooting<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>a)run iotbx.phil
cif_link.params (this checks if the syntax is right)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>b) check .eff file the links
should be added there. You can also check the . geo file if you see anything
strange.<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>c)Having unknown to
phenix.refine item in PDB file (novel ligand, etc... (BMA is also not there) ).
phenix.refine uses the CCP4 Monomer Library as the source of stereochemical
information for building geometry restraints and reporting statistics. If
phenix.refine is unable to match an item in input PDB file against the Monomer
Library it will stop with "Sorry" message explaining what to do and
listing the problem atoms. If this happened, it is necessary to obtain a cif
file (parameter file, describing unknown molecule) by either making it manually
or having eLBOW program to generate it:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>phenix.elbow model.pdb
--do-all --output=all_ligands<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>this will ask eLBOW to
inspect the model_new.pdb file, find all unknown items in it and create one cif
file for them all_ligands.cif. Alternatively, one can specify a three-letters
name for the unknown residue:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>phenix.elbow model.pdb
--residue=MAN --output=man<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>!Check the file if
everything is ok!<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>Once the cif file is
created, the new run of phenix.refine will be:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>phenix.refine model.pdb
data.pdb man.cif<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>Consult eLBOW documentation
for more details. </span><span style='font-size:10.0pt;font-family:"Courier New"'>Check
the file<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span
lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><span style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'>From the command line
everything is perfect now, but as I also want to know how to do this with the
gui (version 1.6-289), I added the files BMA.cif file and the
apply_cif_link.params together with my coordinates and the mtz in the Input
files. But I get following error message:<o:p></o:p></span></p>
<p class=MsoListParagraph><span lang=EN-US 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'><img width=507 height=210 id="Grafik_x0020_0"
src="cid:image001.png@01CAB66A.DFAA50B0" alt="Screenshot-PHENIX errorcif.png"></span><span
lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Is this a Bug?<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks again and kind regards Georg.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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