<div dir="ltr"><div>Dear all,</div><div><br></div>To those who are interested in the phenix.polder tool:<div><br></div><div>An "official" announcement and a detailed description on how to run phenix.polder will come soon. However, here is some more information for those who already want to try the tool.<br><div><br></div><div>Polder calculates omit maps by excluding the bulk solvent mask to flood into the area of the atom selection. So they might be effective for atom selections in binding pockets and around the surface of the protein. Atom selection can be f.ex. a ligand or a protein residue. </div><div><br></div><div><div>How to run: <span style="font-size:12.8px">phenix.polder model.pdb data.mtz selection="chain A and resseq 123"</span></div></div><div><span style="font-size:12.8px"><br></span></div><div>The selection should be one ligand or one residue. I do not recommend choosing a very large selection, such as several ligands or large number of residues at once. <span style="font-size:12.8px"><br></span></div><div><br></div><div>To look at the map, open "polder_map_coeffs.mtz" (which has been created by polder) in COOT, using the "Open MTZ, mmCIF, fcf or phs" option, and by checking the box "Is a difference map". Then choose map coefficients "<span style="font-family:arial,helvetica,sans-serif;color:black">mFo-</span><span style="font-family:arial,helvetica,sans-serif;color:black">DFc_polder</span><span style="font-family:arial,helvetica,sans-serif;color:black">" and corresponding phases.</span></div><div><span style="font-family:arial,helvetica,sans-serif;color:black">If you want to compare to an omit map which has been calculated by deleting the atom selection from the model, open "</span><span style="font-family:arial,helvetica,sans-serif;color:black">mFo-</span><span style="font-family:arial,helvetica,sans-serif;color:black">DFc_omit</span><span style="color:black;font-family:arial,helvetica,sans-serif">".</span></div><div><span style="color:black;font-family:arial,helvetica,sans-serif"><br></span></div><div><span style="color:black;font-family:arial,helvetica,sans-serif">Let me know if you have questions. </span></div><div><span style="color:black;font-family:arial,helvetica,sans-serif"><br></span></div><div><span style="color:black;font-family:arial,helvetica,sans-serif">Best wishes,</span></div><div><span style="color:black;font-family:arial,helvetica,sans-serif"><br></span></div><div><span style="color:black;font-family:arial,helvetica,sans-serif">Dorothee</span></div><div><br></div><div><br></div><div><br></div><div><br></div><div>
<div style="margin-top:0pt;margin-bottom:6pt;margin-left:0.31in;direction:ltr"><br></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Feb 25, 2016 at 9:09 AM, 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">Hi Huanwang,<br>
<br>
it needs to contain diffraction data, Fobs (Iobs) and (optionally) free-r flags.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On 2/25/16 08:55, Huanwang Yang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Pavel,<br>
<br>
Thanks you so much for the new tool which will be useful to the density validation.<br>
<br>
I have a question about the mtz file that is provided to the phenix.polder.<br>
1. Does it have to contain the map coefficients such as FOFCWT/PHFOFCWT?<br>
2. If the mtz must contains the FOFCWT/PHFOFCWT, do you have a simple tool that will calculate the map coefficients using your bulk solvent method?<br>
<br>
Thanks a lot.<br>
<br>
Huanwang<br>
<br>
On 02/25/2016 11:29 AM, Pavel Afonine wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Alex,<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This is not exactly phenix specific, but I was wondering what are some commonly used methods to determine and validate the presence/occurrence of multiple conformations for a given amino acid?<br>
</blockquote>
<br>
I just realized it myself yesterday that most efficient (in terms of finding answer) way is to use new Phenix tool called phenix.polder (a new tool being developed in our team in order to better visualize weak densities in residual Fo-Fc maps), which is available in latest nightly build. Example:<br>
<br>
phenix.polder model.pdb data.mtz selection="chain A and resseq 123"<br>
<br>
where "chain A and resseq 123" selects residue in question (this assumes you have placed one copy of residue conformer).<br>
<br>
Pavel<br>
<br>
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</blockquote>
<br>
<br>
</blockquote>
<br>
</div></div></blockquote></div><br></div>