<div dir="ltr">Hi Ian,<div><br></div><div>Your critical anomalous stats are:</div><div><br></div><div>1. CC-1/2 ... half-dataset correlation for a SAD dataset. Should be above about 0.3 in resolution range of interest. You can calculate this with phenix.anomalous_signal</div><div><br></div><div>2. Anomalous correlation between wavelengths. You get this if you run phenix.autosol with MAD data and look at the scaling log file. It will llist each pair-wise comparison of wavelengths and a resolution breakdown of CC values. Again, looking for 0.3 between peak and remote to indicate that data are strong to a particular resolution.</div><div><br></div><div>3. If you have independent data sets (different anomalous atom for example), and each one has a "solution", you can often get a very good idea of whether both are correct by calculating the map-map correlation (phenix.get_cc_mtz_mtz). If one is wrong, you get a low value (like 0.05); this tells you nothing. If the datasets are really the same you may get a very high number like 0.7 and that tells you nothing as well. But if both are right, and they are independent, you might get a value like 0.2 - 0.5. This is very encouraging if you get it. You can use this trick for all kinds of structure solution tries and you can automate it to compare everything in sight. The key is independence...</div><div><br></div><div>AutoSol won't really let you choose the number of sites...even if you tell it 5, it will look for more.</div><div><br></div><div>I'd say...always try hard with existing data and if you have the opportunity to get SeMet data, pursue that in parallel until you get it or you solve the structure with existing data.</div><div><br></div><div>All the best,</div><div>Tom T</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Mar 12, 2018 at 1:17 PM, Ian Slaymaker <span dir="ltr"><<a href="mailto:iscrystallo@gmail.com" target="_blank">iscrystallo@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">Hello Phenixbb,<div><br><div>I've been out of the crystallography game for a few years and was hoping for some suggestions.<br><div>I'm trying to phase a structure (~1200aa protein:DNA complex) with native data out to 2.0A and SAD/MAD data out to 3.0-2.6. I'm trying to use Br/I soaking while I wait for Sel-Met crystals to grow. </div></div><div><br></div><div>I'm collecting 1800 frames at a synchrotron and scaling together multiple MAD wavelength <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">sets (30 degree inverse wedges) collected from the same crystal </span>with phenix.scale_and_merge to achieve >85% anomalous data (determined by xtriage). Anomalous signal of the merged data is around 10 at the 3.5 angstrom shell. I'm keeping an eye on the merging statistics, but I'm not sure what the critical stats to monitor are. </div><div><br></div><div>AutoSol has given me a a few possible solutions, finding between 3 and 8 sites for MAD and SAD sets(I'm letting AutoSol decide how many to find) with Resolve Rfactors around 0.34, but low map skew (<1 and sometimes negative). I've tried using the initial sites to search for additional Br sites, but with no luck, and the density isn't good enough to build anything into. I'm doing hyss searches with various resolution cutoffs and continue to get the same/similar uninterpretable density with very few heavy atom sites found. </div><div><br></div><div>My questions:</div><div>What are the critical stats to look at when merging data for anomalous signal? </div><div>Are there parameters to explore in AutoSol to identify more heavy atom sites?</div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Should I accept that I need to wait for new crystals to grow or keep charging ahead with this data, encouraged by some promising numbers by AutoSol? </span><br></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Thank you in advance for the suggestions. </span></div><span class="HOEnZb"><font color="#888888"><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">-Ian</span></div><div><br></div><div><br></div><div><br></div></font></span></div></div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.<wbr>org</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Thomas C Terwilliger<div>Laboratory Fellow, Los Alamos National Laboratory</div><div>Senior Scientist, New Mexico Consortium</div><div>100 Entrada Dr, Los Alamos, NM 87544</div><div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div><div>Tel: 505-431-0033</div><div><br></div></div></div></div></div></div></div></div>
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