<div dir="ltr"><p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif"">Thank you very much for your replies.</span></p><p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif""><br></span></p><p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif""> Here is what I did:</span></p>
<p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif"">1)I rerun xdsconv again with Friedls law=false in order
to get the mtz file with the F(+) and F(-) columns (new.mtz). <span style> </span></span></p>
<p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif"">2) I used my pdb file from the last refinement together
with the new.mtz file as input for “Calculate maps” in Phenix and selected the
option for anomalous map. </span></p>
<p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif"">Now I obtained the ANOM PHANOM map. I hope this is
correct…</span></p>
<p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif"">In the anomalous map the largest density is in the Mo and
Fe atoms. There is no density in the S of SO3 or SO4 groups, so, this will not
help me to decide whether there are SO3 groups in the structure (because for the
SO4 I have no doubt).</span></p>
<pre><span style="font-family:"Arial","sans-serif"">However, while searching the mailling list I foud this post <a href="http://www.phenix-online.org/pipermail/phenixbb/2009-September/013799.html">http://www.phenix-online.org/pipermail/phenixbb/2009-September/013799.html</a> which <br>worried me. Should I have used from the beginning this “new” mtz file with F+/F- in order to obtain anomalous differences map at each <br>refinement step? Do you think that I should go back, transfer the R-free flags to my new mtz file and repeat all the refinements?<br><br></span></pre><pre><span style="font-family:"Arial","sans-serif"">Best regards,<br></span></pre><pre><span style="font-family:"Arial","sans-serif"">Alexandra<br></span></pre><pre><span style="font-family:"Arial","sans-serif""></span></pre>
<p class="MsoNormal"><span style="font-size:10pt;line-height:115%;font-family:"Arial","sans-serif""> </span></p>
<div class="gmail_extra"><br><div class="gmail_quote">2015-06-17 16:59 GMT+01:00 Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Alexandra,<br>
<br>
to get anomalous difference map you do not need to do anything
special: phenix.refine calculates this map by default as long as
your input data are Fobs(+) and Fobs(-) or Iobs(+) and Iobs(-).<br>
<br>
Refining occupancy of Mo may not be a bad idea given it is likely to
be partially occupied.<br>
<br>
Pavel<div><div class="h5"><br>
<br>
<div>On 6/17/15 06:04, Alexandra Marques
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<p class="MsoNormal">Hi,</p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal">I am in the last refinement steps of a MR
model and I want
to calculate an anomalous difference map<span>
</span>essentially to confirm the presence of a sulfite
molecule and to locate vanadium
(present in soaking solution). I read that it is necessary to
have a mtz file
with anomalous data (i.e. F+,F- or I+,I-). However, my data
was collected at “normal”
wavelenght (0.97) and it was processed with XDS considering
Friedls law= true
and my mtz file contain the following columns: H K L FP SIGFP.
So, can I still
calculate a anomalous difference map based on my data?</p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal">Since I also have a Mo atom in the active
site can I try to
refine its occupancy by using the option “anomalous groups” in
the refinement
strategy? <br>
</p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal">Thank you very much, </p>
<span style="font-size:11pt;line-height:115%;font-family:"Calibri","sans-serif"">Alexandra</span></div>
<br>
<fieldset></fieldset>
<br>
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