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<p class=MsoPlainText><span lang=EN-US>Dear All, <o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-US>I�m quite new to crystallography and I�m
refining a structure with ASN-NAG-NAG-BMA attached and already got help from Blaine
who told me how to do it, but I�m making a small mistake somewhere and can�t
figure out what I�m doing wrong. Must be just one paranthesis or so, I guess.<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-US>In command line just for testing I put:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>phenix.refine
refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb cif_link.params BMA.cif strategy=individual_sites+individual_adp
main.number_of_macro_cycles=2 --overwrite<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>where
I put in cif_link.params as suggested in the mailing list <a
href="http://www.phenix-online.org/pipermail/phenixbb/2009-November/002837.html">http://www.phenix-online.org/pipermail/phenixbb/2009-November/002837.html</a>
with and without paranthesis at the beginning<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>}�
<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = NAG-ASN<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_1 = chain A and resname NAG and resid 500<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>�
�����residue_selection_2 = chain A and resname ASN and resid 297<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
}<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = BETA1-4<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_1 = chain A and resname NAG and resid 500<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_2 = chain A and resname NAG and resid 501<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
}<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = BETA1-4<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_1 = chain A and resname NAG and resid 501<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_2 = chain A and resname BMA and resid 502<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
}<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = ALPHA1-3<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_1 = chain A and resname BMA and resid 502<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_2 = chain A and resname MAN and resid 503<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>and
suggested by Blaine with and without paranthesis at the beginning<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>refinement.pdb_interpretation.apply_cif_link
{<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = NAG-ASN<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_1 = chain A and resname NAG and resid 500<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_2 = chain A and resname ASN and resid 297<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
}<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
refinement.pdb_interpretation.apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = BETA1-4<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_1 = chain A and resname NAG and resid 500<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_2 = chain A and resname NAG and resid 501<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
}<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
refinement.pdb_interpretation.apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = BETA1-4<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>�
�����residue_selection_1 = chain A and resname NAG and resid 501<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_2 = chain A and resname BMA and resid 502<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
}<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>����
refinement.pdb_interpretation.apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
data_link = ALPHA1-3<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_1 = chain A and resname BMA and resid 502<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>������
residue_selection_2 = chain A and resname MAN and resid 503<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>I
see in the .geo file that the residues are not bonded, and also in the .eff
file that these lines are not added there, which should be done I guess, I put
the info also direct into the .def file but I get the same problem?<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>By
the way it shouldn�t matter which name I give to this file as long as the
extension is correct?<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>Thank
you very much and all the best, Georg.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=DE>-----Urspr�ngliche Nachricht-----<br>
Von: phenixbb-bounces@phenix-online.org
[mailto:phenixbb-bounces@phenix-online.org] Im Auftrag von Ursula
Schulze-Gahmen<br>
Gesendet: Dienstag, 23. Februar 2010 19:20<br>
An: phenixbb@phenix-online.org<br>
Betreff: [phenixbb] weights optimization, add hydrogens</span><o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>I am refining a 2.0 A structure in Phenix using mostly
the graphical <o:p></o:p></p>
<p class=MsoPlainText>interface. The maps are very good and the R factors are
low <o:p></o:p></p>
<p class=MsoPlainText>(0.208/0.173). But the geometry is not so great with bond
deviations of <o:p></o:p></p>
<p class=MsoPlainText>0.208 and Angle deviations of 1.85.� What is the best
thing to do to try <o:p></o:p></p>
<p class=MsoPlainText>to improve the geometry. Should I try to optimize the
weights?<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>The other question is about adding hydrogens to the
model. I did add <o:p></o:p></p>
<p class=MsoPlainText>them in a previous refinement cycle. After rebuilding the
model in coot, <o:p></o:p></p>
<p class=MsoPlainText>most of the model still has the hydrogens in the input
file for the next <o:p></o:p></p>
<p class=MsoPlainText>refinement cycle, but some residues and waters don't have
hydrogens. <o:p></o:p></p>
<p class=MsoPlainText>When I tried to add hydrogens again to the model, I got
an error message <o:p></o:p></p>
<p class=MsoPlainText>about atoms being to close. Does Phenix know where to add
hydrogens if <o:p></o:p></p>
<p class=MsoPlainText>the input model has already hydroegns on many residues?<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Thanks<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Ursula<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>-- <o:p></o:p></p>
<p class=MsoPlainText>Ursula Schulze-Gahmen, PhD.<o:p></o:p></p>
<p class=MsoPlainText>QB3, Tjian Lab<o:p></o:p></p>
<p class=MsoPlainText>MCB, 16 Barker Hall #3204<o:p></o:p></p>
<p class=MsoPlainText>University of California Berkeley<o:p></o:p></p>
<p class=MsoPlainText>Berkeley, CA 94720-3204<o:p></o:p></p>
<p class=MsoPlainText>Phone: (510) 642 8258<o:p></o:p></p>
<p class=MsoPlainText>uschulze-gahmen@lbl.gov<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>_______________________________________________<o:p></o:p></p>
<p class=MsoPlainText>phenixbb mailing list<o:p></o:p></p>
<p class=MsoPlainText>phenixbb@phenix-online.org<o:p></o:p></p>
<p class=MsoPlainText>http://phenix-online.org/mailman/listinfo/phenixbb<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
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