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Hi Chris,<br>
<br>
Your selection is 'empty' because your NAG is not resid 122 but 834.
Your ASN has resid 122.<br>
<br>
You'll have to come to something like this; this correctly makes the
connections you want;<br>
<br>
<br>
apply_cif_link {<br>
data_link = "NAG-ASN"<br>
residue_selection_1 = "chain A and resname NAG and resid 834"<br>
residue_selection_2 = "chain A and resname ASN and resid 122"<br>
}<br>
apply_cif_link {<br>
data_link = "BETA1-4"<br>
residue_selection_1 = "chain A and resname NAG and resid 835"<br>
residue_selection_2 = "chain A and resname NAG and resid 834"<br>
}<br>
<br>
HTH<br>
<br>
Jonathan Elegheert<br>
Ghent University<br>
<br>
Op 01/06/10 13:44, Chris Ulens schreef:
<blockquote
cite="mid:968B196D-078B-44A0-BEF4-ED687DD61221@med.kuleuven.be"
type="cite">Thanks for the feedback.
<br>
I would like to refine a NAG-NAG chain attached to residue Asn122 in my
structure. There are 5 identical subunits.
<br>
Could you verify my .params file?
<br>
I get the following error:
<br>
Empty atom selection
<br>
refinement.pdb_interpretation.apply_cif_link.residue_selection_1="chain
A and resname NAG and resid 122"
<br>
<br>
Thanks.
<br>
-Chris
<br>
<br>
<br>
<br>
<br>
On 31 May 2010, at 21:34, Georg Mlynek wrote:
<br>
<br>
<blockquote type="cite">Dear Chris, this did it for me.
<br>
<br>
<br>
Create a file which you can call whatever you want even the extension
<br>
doesn't matter. E.g.: cif_link.params
<br>
<br>
Put in this file your links: (Which Atom of residue1 will be connected
to
<br>
which Atom in residue2 is already defined in mon_lib_list.cif)
<br>
<br>
<br>
<br>
refinement.pdb_interpretation.apply_cif_link {
<br>
data_link = NAG-ASN
<br>
residue_selection_1 = chain A and resname NAG and resid 500
<br>
residue_selection_2 = chain A and resname ASN and resid 297
<br>
}
<br>
refinement.pdb_interpretation.apply_cif_link {
<br>
data_link = BETA1-4
<br>
residue_selection_1 = chain A and resname NAG and resid 500
<br>
residue_selection_2 = chain A and resname NAG and resid 501
<br>
}
<br>
refinement.pdb_interpretation.apply_cif_link {
<br>
data_link = BETA1-4
<br>
residue_selection_1 = chain A and resname NAG and resid 501
<br>
residue_selection_2 = chain A and resname BMA and resid 502
<br>
}
<br>
refinement.pdb_interpretation.apply_cif_link {
<br>
data_link = ALPHA1-3.
<br>
<br>
residue_selection_1 = chain A and resname BMA and resid 502
<br>
residue_selection_2 = chain A and resname MAN and resid 503
<br>
}
<br>
<br>
4) add this file in the GUI
<br>
<br>
<br>
Or run % phenix.refine model.pdb data.hkl cif_link.params
<br>
<br>
<br>
5)Trouble shooting
<br>
<br>
a)run iotbx.phil cif_link.params (this checks if the syntax is right)
<br>
<br>
b) check .eff file the links should be added there. You can also check
the .
<br>
geo file if you see anything strange.
<br>
<br>
c)Having unknown to phenix.refine item in PDB file (novel ligand,
etc...
<br>
(BMA is also not there) ). phenix.refine uses the CCP4 Monomer Library
as
<br>
the source of stereochemical information for building geometry
restraints
<br>
and reporting statistics. If phenix.refine is unable to match an item
in
<br>
input PDB file against the Monomer Library it will stop with "Sorry"
message
<br>
explaining what to do and listing the problem atoms. If this happened,
it is
<br>
necessary to obtain a cif file (parameter file, describing unknown
molecule)
<br>
by either making it manually or having eLBOW program to generate it:
<br>
<br>
phenix.elbow model.pdb --do-all --output=all_ligands
<br>
<br>
this will ask eLBOW to inspect the model_new.pdb file, find all unknown
<br>
items in it and create one cif file for them all_ligands.cif.
Alternatively,
<br>
one can specify a three-letters name for the unknown residue:
<br>
<br>
phenix.elbow model.pdb --residue=MAN --output=man
<br>
<br>
!Check the file if everything is ok!
<br>
<br>
<br>
Please correct if this is not ok, or there is an easier way now.
<br>
<br>
Kind regards George.
<br>
<br>
<br>
-----Ursprüngliche Nachricht-----
<br>
Von: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
<br>
[<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>] Im Auftrag von Chris Ulens
<br>
Gesendet: Monday, May 31, 2010 9:14 PM
<br>
An: PHENIX user mailing list
<br>
Betreff: Re: [phenixbb] NAG-NAG description
<br>
<br>
Dear glycobiologists and phenixfriends.
<br>
<br>
I am trying to refine a NAG-NAG chain attached to an Asn122 in my
<br>
(pentameric) structure.
<br>
What is the proper description in the cif_link.params that is the
<br>
equivalent of the pdb description pasted below that phenix so kindly
<br>
ignores?
<br>
Also, what is the proper way to define the cif_link.params file in the
<br>
GUI?
<br>
<br>
Thank you.
<br>
-Chris
<br>
<br>
<br>
LINK ND2 ASN A 122 C1 NAG A 834 1555
<br>
1555 1.37
<br>
LINK O4 NAG A 834 C1 NAG A 835 1555
<br>
1555 1.43
<br>
LINK ND2 ASN B 122 C1 NAG B 834 1555
<br>
1555 1.37
<br>
LINK O4 NAG B 834 C1 NAG B 835 1555
<br>
1555 1.43
<br>
LINK ND2 ASN C 122 C1 NAG C 834 1555
<br>
1555 1.37
<br>
LINK O4 NAG C 834 C1 NAG C 835 1555
<br>
1555 1.43
<br>
LINK ND2 ASN D 122 C1 NAG D 834 1555
<br>
1555 1.37
<br>
LINK O4 NAG D 834 C1 NAG D 835 1555
<br>
1555 1.43
<br>
LINK ND2 ASN E 122 C1 NAG E 834 1555
<br>
1555 1.37
<br>
LINK O4 NAG E 834 C1 NAG E 835 1555
<br>
1555 1.43
<br>
<br>
---------------------------------------------------
<br>
Chris Ulens, Ph.D.
<br>
Lab of Structural Neurobiology
<br>
Department of Molecular Cell Biology
<br>
Campus Gasthuisberg, ON1
<br>
Herestraat 49, PB 601
<br>
B-3000 Leuven
<br>
Belgium
<br>
e <a class="moz-txt-link-abbreviated" href="mailto:chris.ulens@med.kuleuven.be">chris.ulens@med.kuleuven.be</a>
<br>
t +32 16 345812
<br>
f +32 16 345699
<br>
w <a class="moz-txt-link-freetext" href="http://www.xtal.be">http://www.xtal.be</a>
<br>
<br>
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</blockquote>
<br>
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