<div dir="ltr">Yarrow<div><br></div><div>The inputs are likely telling it to form the bond as it's not an automatic thing. Please send all inputs to Pavel and I, off-line.</div><div><br></div><div>Cheers</div><div><br>
</div><div>Nigel</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jun 23, 2014 at 6:03 PM, Yarrow Madrona <span dir="ltr"><<a href="mailto:amadrona@uci.edu" target="_blank">amadrona@uci.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi again,<div><br></div><div>So the problem has been solved by adding a bond line into the CIF that explicitely tells phenix that the "bond" should be 4 angstroms instead of 2.1. But I don't understand why Phenix would somehow see that these atoms should be bonded together. This is a phenyl immidazole ligand with two nitrogens, one of which is about 1.9 angstroms from the iron (a real coordination). The other is about 4 angstroms. Why does phenix seem to want to assign a bond between the nitrogen further away?</div>
<span class="HOEnZb"><font color="#888888">
<div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">-Yarrow</font></span><div class=""><br><br>On Monday, June 23, 2014, Yarrow Madrona <<a href="mailto:amadrona@uci.edu" target="_blank">amadrona@uci.edu</a>> wrote:<br>
</div><div><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:15.555556297302246px">Hello,</span><div style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br></div><div style="font-family:arial,sans-serif;font-size:15.555556297302246px">
I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get:</div>
<div style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br></div><div style="font-family:arial,sans-serif;font-size:15.555556297302246px"><div>bond pdb="FE HEM A 410 "</div><div> pdb=" N3 CPZ A 500 "</div>
<div> ideal model delta sigma weight residual</div><div> 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01</div></div><div style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br></div><div style="font-family:arial,sans-serif;font-size:15.555556297302246px">
N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc.</div>
<div style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br></div><div style="font-family:arial,sans-serif;font-size:15.555556297302246px">Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.</div>
</div>
</blockquote></div></div></div>
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<br></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 : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
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