<div dir="ltr">Hi Pavel<div><br></div><div>Thanks again for the advice. I have run Polder map on two of the nucleotides in doubt. The CC for one of them:</div><div>N1:CC(1,2): 0.5610</div><div>CC(1,3): 0.6212</div><div>CC(2,3): 0.5193</div><div><br></div><div>Peak CC:</div><div>CC(1,2): 0.5444</div><div>CC(1,3): 0.5798</div><div>CC(2,3): 0.4921</div><div><br></div><div>The embarrassing issue here is that these two nucleotides make complete sense biologically if they turn out to be flexible. Will the high B-factor hinders the calculation of CC in Polder map? Meanwhile, I notice there is a column labeled 'q' in the log output like the below<br></div><div><br></div><div><div>q D(1,2) D(1,3) D(2,3)</div><div>0.10 0.4162 0.7689 0.6533</div><div>0.20 0.4748 0.6926 0.6796</div><div>0.30 0.5252 0.6516 0.6466</div><div>0.40 0.6243 0.6590 0.6937</div><div>0.50 0.6576 0.6160 0.7034</div><div>0.60 0.6851 0.5420 0.6807</div><div>0.70 0.7606 0.5029 0.6442</div><div>0.80 0.8422 0.4325 0.6959</div><div>0.90 0.9365 0.4567 0.7226</div><div>0.91 0.9783 0.4447 0.7750</div><div>0.92 0.9614 0.4666 0.7352</div><div>0.93 0.9591 0.4955 0.7513</div><div>0.94 0.9594 0.5258 0.8026</div><div>0.95 0.9639 0.5805 0.7558</div><div>0.96 1.0026 0.6504 0.8130</div><div>0.97 0.9655 0.6079 0.7867</div><div>0.98 1.0087 0.9025 0.8495</div><div>0.99 0.8934 0.9460 0.8934</div></div><div><br></div><div>Could you enlighten me as to the meaning of these or where I could go for relevant readings?</div><div><br></div><div>Many thanks indeed.</div><div><br></div><div>Kind regards</div><div><br></div><div><div class="gmail_extra"><div><div class="gmail_signature"><div dir="ltr"><div dir="ltr"><div style="font-size:12.7273px"><font color="#000000">Sam <br></font></div></div></div></div></div>
<div class="gmail_extra"><br></div><br><div class="gmail_quote">On 4 June 2017 at 11:23, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Sam,<span class="gmail-"><br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
I have tried Polder Map as well as the conventional SA-OMIT map. My feeling is that the conventional way gives better map for the ligand at the 'good' region than Polder, but neither way improves density at the 'poor' region.<br>
</blockquote>
<br></span>
I'd say it's more about getting convincing map rather than (artistically) looking better one. If three CC numbers that Polder map tool reports are in favor of the ligand then this is what you've got. By design, any sort of OMIT map is expected to appear worse than say usual 2mFo-DFc map (it is naive to expect that by removing bits of model you get a better looking map).<br>
<br>
Both methods you quote are to show you the map, not to improve the model so that in turn you get an improved map.<span class="gmail-HOEnZb"><font color="#888888"><br>
<br>
Pavel<br>
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