<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div>Hi Ian, </div><div><br data-mce-bogus="1"></div><div><div>Thank you for your answer.</div>I definitely agree with you, I know that and I am actually working with the Fs (especially to being able to use buster).</div><div>My question was actually a more general point of view about that, like opening a discussion about the influence of the negative intensity and about the different existing way to deal with them. </div><div><br data-mce-bogus="1"></div><div>Cheers, </div><div><br data-mce-bogus="1"></div><div>Nicolas</div><div><br></div><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>De: </b>"Ian Tickle" <ianjt05@gmail.com><br><b>À: </b>"Nicolas Foos" <nicolas.foos@ibs.fr><br><b>Cc: </b>"buster-discuss" <buster-discuss@globalphasing.com><br><b>Envoyé: </b>Mardi 22 Juin 2021 13:04:29<br><b>Objet: </b>Re: [buster-discuss] two questions : one about negative reflections and one about Simulated annealing<br></div><div><br></div><div data-marker="__QUOTED_TEXT__"><div dir="ltr"><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">Hi Nicolas</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">Sorry a correction to my first reply:</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">"Fs unlike intensiities cannot be non-negative by definition"<br></div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">should of course read</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">"Fs unlike intensiities cannot be negative by definition"<br></div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">Too many negatives!</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">Cheers</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">-- Ian</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 22 Jun 2021 at 11:43, Ian Tickle <<a href="mailto:ianjt05@gmail.com" target="_blank" rel="nofollow noopener noreferrer">ianjt05@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"><div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">Hi Nicolas</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">I should have included a link to the StarAniso webserver in case you are not aware of it:</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif"><a href="https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi" target="_blank" rel="nofollow noopener noreferrer">https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi</a><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">There you can get a lot more information (and maybe even submit your data to it!).</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">Cheers</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div><div class="gmail_default" style="font-family:'arial' , sans-serif">-- Ian</div><div class="gmail_default" style="font-family:'arial' , sans-serif"><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 22 Jun 2021 at 11:36, Ian Tickle <<a href="mailto:ianjt05@gmail.com" target="_blank" rel="nofollow noopener noreferrer">ianjt05@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"><div dir="ltr"><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif">Hi Nicolas</div><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif">As far as I know, Buster doesn't have a Simulated Annealing option, but maybe the Buster developers will have more to say on that.</div><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif">On your second question, there's an important step between getting the merged intensities and performing the refinement with Buster. Again as far as I know Buster only uses amplitudes (Fs) as input. Fs unlike intensiities cannot be non-negative by definition. So we need to convert all the merged intensities including negative ones to positive Fs. This is usually done by French & Wilson Bayesian estimation:</div><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif"><a href="https://warwick.ac.uk/fac/sci/statistics/staff/academic-research/french/publications/bayes_impact_french_wilson.pdf" target="_blank" rel="nofollow noopener noreferrer">https://warwick.ac.uk/fac/sci/statistics/staff/academic-research/french/publications/bayes_impact_french_wilson.pdf</a><br></div><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif">Also see the reference to the original 1978 paper cited there.</div><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif">This algorithm, or a modification of it, is implemented, among others, in the Truncate, CTruncate and StarAniso programs. For example, StarAniso computes the Fs using a very accurate numerical method instead of using table look-ups, and takes into account the effect of anisotropy on the Bayesian prior.</div><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif">Best wishes</div><div style="font-family:'arial' , sans-serif"><br></div><div style="font-family:'arial' , sans-serif">-- Ian</div><div style="font-family:'arial' , sans-serif"><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 22 Jun 2021 at 10:29, Nicolas Foos <<a href="mailto:nicolas.foos@ibs.fr" target="_blank" rel="nofollow noopener noreferrer">nicolas.foos@ibs.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"><div><div style="font-family:'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"><blockquote><div>Dear buster users and developers, </div><br><div>I have two questions : one simple : is it possible to perform a simulated annealing using buster. I didn't see anything like that in the manual, but maybe I miss it.</div><br><div>The second question : how autoBuster handle the negative reflections present in the data file ? </div><div>- Does it ignore them ? </div><div>- Does it fill them ? </div><div>- Does it set them to zero ? </div><div>What's you opinion about that point, should we use them or not. I would be glad to have your opinion about that point. </div><br><div>To let you know a bit more : I am working on time resolve project. The Data were originally collected in XFEL, then processed using CrystFel. And then based on Fo(state1)-Fo(state2) difference map calculation, I did an extrapolation to refine the model. The data which generates my questions are the Extrapolated ones. </div><br><div>I am fully open to any comments.</div><br><div>All the best, </div><br><div>Nicolas Foos</div><br></blockquote></div></div>_______________________________________________<br>
buster-discuss mailing list<br>
<a href="mailto:buster-discuss@globalphasing.com" target="_blank" rel="nofollow noopener noreferrer">buster-discuss@globalphasing.com</a><br>
<a href="https://www.globalphasing.com/mailman/listinfo/buster-discuss" rel="noreferrer nofollow noopener noreferrer" target="_blank">https://www.globalphasing.com/mailman/listinfo/buster-discuss</a></blockquote></div>
</blockquote></div></div>
</blockquote></div><br></div></div></body></html>