<div dir="ltr"><div class="gmail_extra">On Thu, Apr 4, 2013 at 11:22 AM, Georg Mlynek <span dir="ltr"><<a href="mailto:georg.mlynek@univie.ac.at" target="_blank">georg.mlynek@univie.ac.at</a>></span> wrote:<br><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">1a. Providing the XDS_ASCII.HKL to phenix tableI works perfect, however there are no values written for CC1/2. The same file in phenix.merging_statistics I get the CC1/2. Am I missing something?<br>
</blockquote><div><br></div><div style>No, I am. �Sorry, will fix this ASAP.</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
1b. The only value phenix tablel one takes from INTEGRATE.LP (i guess �CORRECT.LP will work too) is the wavelength - true?<br></blockquote><div><br></div><div style>I'm not sure which specific files from XDS will actually work, but in general, yes, the wavelength is the only thing I extract from the integration log file. �(Unfortunately this is the one parameter on which we really depend on logfiles, since the wavelength is - inexplicably - not reliably propagated in reflection files.)</div>
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2. I see some negative density around the seleniums in my selenomethionine labeled protein. I guess this is due to radiation damage. Is the accepted standard to do occupancy refinement for just the sidechain, or just parts of the sidechain, the whole residue �or just leave it like it is.<br>
</blockquote><div><br></div><div style>This seems like a matter of personal preference, but I would definitely *not* refine the occupancy of the entire sidechain unless I was modeling it as a mix of MET and MSE to reflect partial incorporation. �So there are several options:</div>
<div style><br></div><div>1) refine the occupancies for SE atoms alone</div><div>2) leave them alone<br></div><div style>3) refine alternate conformations</div><div style><br></div><div style>I prefer (1), but it's difficult to know exactly what the difference map holes mean; they could simply be Fourier artifacts.</div>
<div style><br></div><div style>A less conventional option is to�refine f' and f'' for the SE atoms, but leave the occupancies at 1. �I'm still a little confused about how f' and occupancy are correlated*, but in my experience the anomalous refinement soaks up most if not all of the difference in occupancy. �The problem right now is that you can't deposit these parameters in the PDB, but hopefully that will change soon.</div>
<div style><br></div><div style>-Nat</div><div style><br></div><div style>(* A follow-up question for more knowledgable folks: could the large dispersive difference at the K edge be reflected as apparent partial occupancy, or am I misunderstanding the effect on scattering?)</div>
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