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<p style="margin:0in;font-family:Calibri;font-size:11pt">Dear phenix users,</p>
<p style="margin:0in;font-family:Calibri;font-size:11pt"> </p>
<p style="margin:0in;font-family:Calibri;font-size:11pt">Starting from the
nightly build dev-2356, a new tool for calculating ligand omit-maps, called
'polder', is included in phenix.</p>
<p style="margin:0in;font-family:Calibri;font-size:11pt"> </p>
<p style="margin:0in;font-family:Calibri;font-size:11pt">Usage:</p>
<p style="margin:0in;font-family:Calibri;font-size:11pt;color:black">phenix.polder model.pdb
data.mtz selection='chain A and
resseq 123’</p>
<p style="margin:0in;font-family:Calibri;font-size:11pt"> </p>
<p style="margin:0in;font-family:Calibri;font-size:11pt">Phenix.polder
calculates omit maps for atom selections by preventing the bulk solvent mask to flood
into the atom selection area and its vicinity. The tool can be useful in cases where
the density of the selected atoms is weak and possibly obscured by bulk solvent. </p>
<p style="margin:0in;font-family:Calibri;font-size:11pt">Polder produces less
biased maps compared to procedures where the atom selection occupancy is set to zero,
and the atoms are included in the solvent mask calculation (in that
case, the resulting difference density can have
similar shape than the selected atoms). Phenix.polder excludes a larger volume from the bulk solvent
and therefore prevents misinterpreting bulk solvent density as omit density.</p>
<p style="margin:0in;font-family:Calibri;font-size:11pt"> </p>
<p style="margin:0in;font-family:Calibri;font-size:11pt"><span style="color:black">If you want to know more about how the tool is working and
to see some examples, have a look at the presentation file: </span><a href="https://www.phenix-online.org/presentations/phenix_polder.pdf">https://www.phenix-online.org/presentations/phenix_polder.pdf</a><span style="color:black">.</span></p>
<p style="margin:0in;font-family:Calibri;font-size:11pt;color:black"> </p>
<p style="margin:0in;font-family:Calibri;font-size:11pt;color:black">The
documentation page can be found here:</p>
<p style="margin:0in;font-family:Calibri;font-size:11pt"><a href="www.phenix-online.org/version_docs/dev-2356/reference/polder.html">www.phenix-online.org/version_docs/dev-2356/reference/polder.html</a></p>
<p style="margin:0in;font-family:Calibri;font-size:11pt;color:black"><br></p>
<p style="margin:0in;font-family:Calibri;font-size:11pt;color:black">Best
wishes,</p>
<p style="margin:0in;font-family:Calibri;font-size:11pt"> </p>
<p style="margin:0in;font-family:Calibri;font-size:11pt">Dorothee</p>
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