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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">I forgot to mention if you use the LLG maps in Phaser, you select the elements that you are looking for and the wavelength of data collection. This is a really powerful feature
because it allows Phaser to specifically look for each of the elements you are interested in (and the answers will be different for each because the f' and f" will be different for the different elements).
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<div>All the best,</div>
<div>Tom T</div>
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<div id="divRpF432242" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Terwilliger, Thomas Charles<br>
<b>Sent:</b> Wednesday, June 17, 2015 11:21 AM<br>
<b>To:</b> Alexandra Marques<br>
<b>Cc:</b> phenixbb@phenix-online.org; Terwilliger, Thomas Charles<br>
<b>Subject:</b> RE: [phenixbb] anomalous difference map calculation<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi Alexandra,
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<div>I think your refinements without the anomalous differences are going to be very similar to those with the anomalous differences, so probably no it is not worth it to go back. <span style="font-size:10pt">However it is worth making sure that you are using
the same test set (R_free_flags) throughout.</span></div>
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<div><span style="font-size:10pt">If you want to get the very best anomalous map possible, then you could use instead Phaser to calculate an LLG map for the anomalous differences. You provide your refined model (without the anomalously-scattering atoms) and
your anomalous data and it can calculate this map for you.</span></div>
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<div><span style="font-size:10pt">To get the LLG map, in the Phenix GUI go to Experimental Phasing and select Phaser-EP. Then select the Phaser mode "MR-SAD phasing". Then put in your model and anomalous data. Then under "Other Settings" scroll down and
check "Output LLG maps". Then run and that should do it! Airlie or Randy might have further comments on this!</span></div>
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<div><span style="font-size:10pt">All the best,</span></div>
<div><span style="font-size:10pt">Tom T</span></div>
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<div id="divRpF198336" style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Alexandra Marques [at.marques@fct.unl.pt]<br>
<b>Sent:</b> Wednesday, June 17, 2015 11:07 AM<br>
<b>Cc:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] anomalous difference map calculation<br>
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<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>
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<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" target="_blank">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>
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<p class="MsoNormal"><span style="font-size:10pt; line-height:115%; font-family:"Arial","sans-serif""> </span></p>
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<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>
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<div bgcolor="#FFFFFF">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>
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Refining occupancy of Mo may not be a bad idea given it is likely to be partially occupied.<br>
<br>
Pavel
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<div>On 6/17/15 06:04, Alexandra Marques wrote:<br>
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<p class="MsoNormal">Hi,</p>
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<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>
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<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?
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<p class="MsoNormal">Thank you very much, </p>
<span style="font-size:11pt; line-height:115%; font-family:"Calibri","sans-serif"">Alexandra</span></div>
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