<div dir="ltr"><div><div><div>Hi Nigel<br><br></div>I was referring to the partial charge in the restraint file, which IMHO should be translated to the model.<br></div><div><br></div>I have a second problem - I'm using the cif file for refinement but the angles and bond lengths still get distorted. These are flagged as outliers in phenix.refine. Why is it not using the values that I input? My resolution is 3.8 A, but I still end up with positive density around all the hemes. In fact, the problems with hemes are the cause of a large majority of my outliers. I did a parallel refinement with and without the restraint file - it doesn't make any difference.<br><br></div>Mohamed<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, May 23, 2015 at 4:47 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">Mohamed<div><br></div><div>I'm not sure what you mean. </div><div><br></div><div>Firstly, I would hope you used the default restraints available in Phenix rather that generate restraints in eLBOW.</div><div><br></div><div>Secondly, are you talking about the formal charge in the model file or the partial charges in the restraints file.</div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>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></div></div><div><div class="h5">
<br><div class="gmail_quote">On Fri, May 22, 2015 at 11:01 PM, mohamed noor <span dir="ltr"><<a href="mailto:mohamed.noor34@gmail.com" target="_blank">mohamed.noor34@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">Sorry to bring up an old thread. While tidying up my model before deposition, I noticed that in eLBOW, the HEM restraint has a charge of 0 for the Fe atom. Shouldn't this be +2 or +3? Usually Fe atom gets reduced by X-ray anyway. Or does this only matter for those doing molecular dynamics?<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 31, 2015 at 10:21 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
On 03/31/2015 02:12 PM, Pavel Afonine wrote:<br>
~~~~~~~~~~~~~~~~<span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
In fact, the C atom is covalently linked to the nearest Cys, so the<br>
HEM side chain should be 'moved' into the density and the green blob<br>
shouldn't be there.<br>
</blockquote>
<br>
Is this link defined anywhere in restraints used in refinement?<br>
<br>
Pavel<br>
</blockquote>
<br></span>
Here is an example of restraints for heme c.<br>
Values are from the high-resolution structure 1C75.<br>
Here residue 501 is the heme of course; and 37, 40, 41, and 160 are<br>
the C,C,H, and M in CxxCH---M heme c binding motif.<br>
I use HEC.cif for the heme parameters, but make sure the bond lengths<br>
in the vinyl groups are consistent with single bonds.<br>
<br>
geometry_restraints.edits {<br>
bond {<br>
action = *add delete change<br>
atom_selection_1 = chain D and resid 501 and name FE<br>
atom_selection_2 = chain D and resid 41 and name NE2<br>
symmetry_operation = None<br>
distance_ideal = 1.99<br>
sigma = 0.1<br>
slack = None<br>
}<br>
bond {<br>
action = *add delete change<br>
atom_selection_1 = chain D and resid 501 and name FE<br>
atom_selection_2 = chain D and resid 160 and name SD<br>
symmetry_operation = None<br>
distance_ideal = 2.33<br>
sigma = 0.1<br>
slack = None<br>
}<br>
bond {<br>
action = *add delete change<br>
atom_selection_1 = chain D and resname CYS and resid 37 and name SG<br>
atom_selection_2 = chain D and resname HEC and resid 501 and name CAB<br>
symmetry_operation = None<br>
distance_ideal = 1.815<br>
sigma = 0.1<br>
slack = None<br>
}<br>
bond {<br>
action = *add delete change<br>
atom_selection_1 = chain D and resname CYS and resid 40 and name SG<br>
atom_selection_2 = chain D and resname HEC and resid 501 and name CAC<br>
symmetry_operation = None<br>
distance_ideal = 1.815<br>
sigma = 0.1<br>
slack = None<br>
}<br>
<br>
<br>
<br>
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