<div dir="ltr">Hi Nigel,<div><br></div><div style>Another question. How do I let phenix.refine know that all atoms in my ligand should have the same occupancy for one conformation? The occupancy refinement in phenix.refine assigned different occupancies to atoms in one conformation. </div>
<div style><br></div><div style>Thanks</div><div style><br></div><div style>Yu</div><div style> <br></div><div style><br></div><div style><br></div><div style><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Tue, Oct 1, 2013 at 6:10 PM, Zhang yu <span dir="ltr"><<a href="mailto:phenixzyfish@gmail.com" target="_blank">phenixzyfish@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thanks</div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I ran<div><br></div><div>phenix.metal_coordination </div><div><br></div><div>and got the attached. Pass it to phenix.refine.</div>
</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Sep 30, 2013 at 6:53 PM, Zhang yu <span dir="ltr"><<a href="mailto:phenixzyfish@gmail.com" target="_blank">phenixzyfish@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nigel,<div><br></div><div>Thanks. Please see attached PDB file. The structure has two molecules in one ASU. Each of molecule contains 6 protein chains and three Nucleic-acid chains (i.e. chain A, B, C, D, E, F, G, H and I for molecule 1; chain K, L, M, N, O, P, Q, R, and S for molecule 2)</div>
<div><br></div><div>There is only one nucleoside-triphosphate and its cognate MG++ in each molecule having alternative conformations (named as conformation A and B). The desired restrains are as follows,</div><div><br></div>
<div>In molecule 1,</div><div><div>atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004</div><div>atom_selection_2 = name OD2 and chain N and resname ASP and resseq 739</div></div><div>distance_ideal = 2.090000<br>
</div><div><br></div><div><div>atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004</div><div>atom_selection_2 = name O3G, B and chain S and resname CMP and resseq 2001</div></div><div>distance_ideal = 2.090000<br>
</div><div><br></div><div><div><div>atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004</div><div>atom_selection_2 = name O1B,B and chain S and resname CMP and resseq 2001</div></div><div>distance_ideal = 2.090000</div>
</div><div><br></div><div><div><div>atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004</div><div>atom_selection_2 = name O1B,A and chain S and resname CMP and resseq 2001</div></div><div>distance_ideal = 2.090000</div>
</div><div><br></div><div><div><div>atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004</div><div>atom_selection_2 = name O1G,A and chain S and resname CMP and resseq 2001</div></div><div>distance_ideal = 2.090000</div>
</div><div><br></div><div>In molecule 2,</div><div><div><div>atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004</div><div>atom_selection_2 = name OD2 and chain D and resname ASP and resseq 739</div>
</div><div>distance_ideal = 2.090000<br></div><div><br></div><div><div>atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004</div><div>atom_selection_2 = name O3G, B and chain I and resname CMP and resseq 2001</div>
</div><div>distance_ideal = 2.090000<br></div><div><br></div><div><div><div>atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004</div><div>atom_selection_2 = name O1B,B and chain I and resname CMP and resseq 2001</div>
</div><div>distance_ideal = 2.090000</div></div><div><br></div><div><div><div>atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004</div><div>atom_selection_2 = name O1B,A and chain I and resname CMP and resseq 2001</div>
</div><div>distance_ideal = 2.090000</div></div><div><br></div><div><div><div>atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004</div><div>atom_selection_2 = name O1G,A and chain I and resname CMP and resseq 2001</div>
</div><div>distance_ideal = 2.090000</div></div></div><div><br></div><div><br></div><div><br></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Sep 30, 2013 at 6:31 PM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Can you send the residues involved?<div><br></div><div>Nigel</div><div><br></div><div>NB. Any files sent to me will be held in strictest confidence.<br>
<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>
On Mon, Sep 30, 2013 at 12:51 PM, Zhang yu <span dir="ltr"><<a href="mailto:phenixzyfish@gmail.com" target="_blank">phenixzyfish@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div>
<div dir="ltr">Hi everyone,<div><br></div><div>My structure contains a metal coordinating to some residues, one of which has alternative conformations. Phenix doesn't pickup the residue with alternative conformation when I tried to generate metal restrains using ready.set.</div>
<div><br></div><div>Any idea? Thanks</div><span><font color="#888888"><div><br></div><div>Yu </div></font></span></div>
<br></div></div>_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
<br></blockquote></div><span><font color="#888888"><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>Phone : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>
Fax : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a>
</font></span></div>
<br>_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
<br></blockquote></div><br></div>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>
Fax : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a>
</div>
</div></div></blockquote></div><br></div>
</div></div></blockquote></div><br></div>