<div dir="ltr">Dave<div><br></div><div>You can try two things. I assume that the ligand is one alt. loc. (say A) and the two waters are another (say B). You can run phenix.refine using the link_metals=True (in 1.10.1) to link the Ca to both the ligand and the waters. If that isn't satisfactory, you can use edits.</div><div><br></div><div><a href="http://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles">www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles</a><br></div><div><br></div><div>If you have any trouble let me have the model file.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Oct 27, 2015 at 6:56 AM, David Briggs <span dir="ltr"><<a href="mailto:drdavidcbriggs@gmail.com" target="_blank">drdavidcbriggs@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 PhenixBB. <div><br></div><div>I have a very minor problem with partial occupancy waters moving out of density during refinement</div><div><br></div><div>I have 2 structures, one apo structure (~1.3Å), one ligand bound (~1.5Å).</div><div><br></div><div>The ligand binding site contains a Calcium ion. In the apo form there are 2 waters co-ordinating this Calcium. In the ligand bound form, these waters are replaced by oxygen atoms within the ligand. </div><div><br></div><div>However, the ligand is only at 0.5 Occupancy as part of the ligand lies on a crystallographic two-fold axis. The ligand itself refines well with occupancy fixed at 0.5, and the Bs are sensible. </div><div><br></div><div>In the 50% of the molecules which don't co-ordinate ligand, two waters must co-ordinate the calcium ion, and in keeping with this, we see that the electron density around these positions is greater than would be expected for the 50% occupancy ligand. So I added 2 0.5 occupancy waters to the model at these positions. </div><div><br></div><div>However, when I run phenix.refine (refining XYZ, real space, occupancy, and individual Bs (isotropic for the ligand & waters - for the protein I use anisotropic Bs) these two 'ghost waters' move out of the electron density and their Bs increase massively.</div><div><br></div><div><b>My questions are:</b></div><div><br></div><div>Is there any way to restrain these waters to their apo positions? Is this the correct approach?</div><div><br></div><div>I had initially thought that reference model restraints might be useful here, but if I understand correctly, reference model restraints cannot be applied to waters - Is this correct?</div><div><br></div><div>If I cannot restrain the waters to the apo positions, would I be justified in fixing (constraining) them? This seems a little extreme and I am loath to do it, but given the isomorphous apo structure, I do have evidence that in the absence of ligand waters do take up these positions. </div><div><br></div><div>Can anyone help?</div><div><br></div><div>Cheers,</div><div><br></div><div>Dave</div><div><br></div><div><br clear="all"><div><div><div dir="ltr"><a href="http://about.me/david_briggs" style="margin:0px;padding:0px;border:0px;outline:0px;font-size:14px;font-family:proxima-nova-1,proxima-nova-2,Tahoma,Helvetica,Verdana,sans-serif;vertical-align:baseline;color:rgb(58,169,233);text-decoration:none;line-height:18.2px" target="_blank"><table border="0" cellpadding="0" cellspacing="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;border-spacing:0px"><tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td colspan="3" style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;font-family:inherit;vertical-align:baseline;height:30px"> </td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td align="left" valign="top" style="padding:0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:top;line-height:1"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><img src="http://d3mod6n032mdiz.cloudfront.net/thumb2/d/a/v/david_briggs/david_briggs-105x70.jpg" alt="David Briggs on about.me" width="105" height="70" style="margin:0px;padding:0px;border:1px solid rgb(238,238,238);outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;display:block"></div></td><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;font-family:inherit;vertical-align:baseline;width:10px"> </td><td align="left" valign="bottom" style="padding:0px 0px 3px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:bottom;line-height:1"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:bold;font-style:inherit;font-size:18px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline;line-height:1;color:rgb(51,51,51)">David Briggs</div><div style="margin:1px 0px 0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-size:12px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline;color:rgb(43,130,173)">about.me/david_briggs</div></td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td colspan="3" style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;font-family:inherit;vertical-align:baseline;height:20px"> </td></tr></tbody></table></a><div style="display:inline-block;width:16px;min-height:16px"> </div></div></div></div>
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