<div dir="ltr"><div class="gmail_extra">Dear Pavel </div><div class="gmail_extra"><br></div><div class="gmail_extra">Thanks for the reply. I am trying to prove the presence of ligand as well as to 'push' some density for the weaker part of the ligand. (This relates to another thread I initiated.) In short density for first part of ligand is very good and can confidently be modelled but not the other part. </div><div class="gmail_extra"><br></div><div class="gmail_extra">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.</div><div class="gmail_extra"><br></div><div class="gmail_extra">There seems less keywords to manipulate in Polder than in the conventional way though.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Best regards</div><div class="gmail_extra"><br></div><div class="gmail_extra">Sam</div><div class="gmail_extra"><br>
<br><div class="gmail_quote">On 3 June 2017 at 21:44, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
I'm not sure I understand the concept of individual selection when
doing composite OMIT map. The whole purpose of composite OMIT map is
to do iterative omits and then put the entire mosaic back into full
map so that each region of the map is "omit". This way you are
expecting to get a less biased map that this map also may appear of
a lesser quality.<br>
<br>
It depends what question you are trying to answer. If you the
question is to prove the presence of a ligand then simply compute
Polder map:<br>
<br>
<a class="m_-4474850670153689240m_8537800689156543130m_-1079847765675300599moz-txt-link-freetext" href="http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf" target="_blank">http://journals.iucr.org/d/iss<wbr>ues/2017/02/00/ba5254/ba5254.p<wbr>df</a><br>
<a class="m_-4474850670153689240m_8537800689156543130m_-1079847765675300599moz-txt-link-freetext" href="https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg/videos" target="_blank">https://www.youtube.com/channe<wbr>l/UCcdI0hfHngWAZLJWynxPQWg/vid<wbr>eos</a><br>
<br>
Pavel <br><div><div class="m_-4474850670153689240m_8537800689156543130h5">
<br>
<div class="m_-4474850670153689240m_8537800689156543130m_-1079847765675300599moz-cite-prefix">On 6/3/17 19:48, Sam Tang wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="m_-4474850670153689240m_8537800689156543130h5">
<div dir="ltr">Dear all
<div><br>
</div>
<div>Sorry for a very basic question about generating an omit
map.</div>
<div><br>
</div>
<div>I am trying to generate a SA-omit map for only my ligand
but not the protein core of my complex. I presume I can use
phenix.composite_omit_map GUI and specify my ligand chain in
Atom Selection? </div>
<div><br>
</div>
<div>All other parameters being the same, I notice that when I
did not select any atom the whole structure was divided to
30-40 regions but when I selected my ligand chain it now
divides into 89 regions. Is there a reason why and is there
any advantage to manually adjust the number of omit regions?</div>
<div><br>
</div>
<div>Many thanks and regards</div>
<div><br clear="all">
<div>
<div class="m_-4474850670153689240m_8537800689156543130m_-1079847765675300599gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div dir="ltr">
<div style="font-size:12.7272720336914px"><font color="#000000">Sam </font></div>
<div style="font-size:12.7272720336914px"><font color="#000000">Biochemistry Programme, School of
Life Sciences, CUHK</font></div>
<div style="font-size:12.7272720336914px"><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
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