Cheers Pavel, 160 water molecules from 330.. <br>P<br><br><div><span class="gmail_quote">On 10/9/07, <b class="gmail_sendername">Pavel Afonine</b> <<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Partha,<br><br>> At your leasure, if you could explain a bit about the water picking<br>
> parameters, that would be great. In my case, for 132 residues and 55%<br>> solvent content, the default setting was picking 330 waters, which is<br>> bit too much I felt. Did change the b_iso_min = 10 and b_iso_max = 40,
<br>> just to see what happens.. (because I thought for ordered water the<br>> later should not be too high..) but I was not sure what the other<br>> parameters mean. Like pick water above 3 sigma, remove below 0.9
sigma<br>> as we are used to from Arp..<br><br>refinement {<br> ordered_solvent {<br> b_iso_min = 1<br> b_iso_max = 50<br> primary_map_cutoff = 3<br> secondary_map_cutoff = 1<br> min_solv_macromol_dist = 1.8
<br> max_solv_macromol_dist = 6<br> min_solv_solv_dist = 1.8<br> }<br>}<br><br>Here are the "most important":<br><br>1) Waters with refined B-factors beyond this interval are removed:<br>(b_iso_min = 1, b_iso_max = 50). I presume you do not refine the
<br>occupancies for water molecules; otherwise there are similar parameters<br>for occupancies as well.<br><br>2) phenix.refine uses two maps to select prospective electron density<br>peaks: mFo-DFc (primary map) and 2mFo-DFc (secondary map).
<br>primary_map_cutoff = 3 and secondary_map_cutoff = 1 define peak heights;<br>default is -- a peak must be higher than 3 sigma for primary map and<br>higher than 1 sigma for secondary map to be considered as a water<br>
pick-candidate. Raising these values will select stronger peaks and<br>obviously will result in lesser number of found waters.<br><br>3) Only peak located within this distance interval from macromolecule<br>are considered (min_solv_macromol_dist =
1.8, max_solv_macromol_dist =<br>6). Some people believe that 6.0A is too generous. You may try to reduce<br>it to lesser values like 3.5...4.5A. Again this will reduce the number<br>of found waters.<br><br>4) Waters separated by less than min_solv_solv_dist =
1.8 are removed.<br><br>The options "2)" and "3)" can have the highest impact on the number of<br>located water molecules. So, I would play with those first and monitor<br>R/Rfree as well.<br><br>The other parameters have higher "expert level" and lesser impact on the
<br>outcome, so I don't explain them until requested.<br><br>Pavel.<br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org
</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></div><br><br clear="all"><br>-- <br>MRC National Institute for Medical Research
<br>Division of Molecular Structure<br>The Ridgeway, NW7 1AA, UK<br>Email: <a href="mailto:pchakra@nimr.mrc.ac.uk">pchakra@nimr.mrc.ac.uk</a><br>Phone: + 44 208 816 2515