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Hi Mark,<br>
<br>
phenix.refine finds potential water peaks looking at mFo-DFc map
(primary map). Then it sorts these peaks by the distances (water-water,
water-other). Then it checks for hydrogen bonding. Finally, it verifies
that the peaks are present at 2mFo-DFc map (secondary map) at given
sigma. Finally finally, the water B-factors (and occupancies, if
requested) are refined separately from refinement of other parameters
in order to get a reasonable starting point for the next refinement
macro-cycle. The procedure is smart enough about cases when your
structure has explicit hydrogen atoms.<br>
<br>
What is crucial is that this procedure is built into refinement, so the
water molecules are updated (added / removed / refined) during
refinement and NOT as a separate step. <br>
<br>
There are various options to refine water with isotropic or anisotropic
B-factors, refine water occupancies, etc. <br>
<br>
We still need to do a better job on NOT picking water into ligand
density. This is in our to-do list and will be done at some point. <br>
<br>
There are a few slides in one of the most recent phenix.refine
presentation that outline most of what I wrote above:<br>
<br>
<a class="moz-txt-link-freetext" href="http://cci.lbl.gov/~afonine/aca2008_knoxville_neutron/phenix_refine_2008_may_31_ACA_final.pdf">http://cci.lbl.gov/~afonine/aca2008_knoxville_neutron/phenix_refine_2008_may_31_ACA_final.pdf</a><br>
<br>
Please let us know if you have any other questions,<br>
Pavel.<br>
<br>
<br>
On 7/31/2008 2:03 PM, Mark Collins wrote:
<blockquote
cite="mid:C8B75E7A-B4AA-44AE-84EC-3D3E2E7098B4@convex.hhmi.columbia.edu"
type="cite">
<div style="margin: 0px;"><font class="Apple-style-span"
face="Helvetica">Hi</font> All</div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">I was just going through the .help section and
website documentation</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">for ordered_solvent. And wonder if somebody
could enlighten me as too</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">the meanings of;</font></div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">ordered_solvent {</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> primary_map_type = mFobs-DFmodel</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> secondary_map_type = 2mFobs-DFmodel</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> h_bond_min_mac = 1.8</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> h_bond_min_sol = 1.8</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> h_bond_max = 3.2</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> }</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> peak_search {</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> map_next_to_model {</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> use_hydrogens = False</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> }</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> max_number_of_peaks = None</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> peak_search {</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> peak_search_level = 1</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> max_peaks = 0</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> interpolate = True</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> min_distance_sym_equiv = None</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> general_positions_only = False</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> min_cross_distance = 1.8</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4"> }</font></div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">What is the difference between the primary and
secondary map? Is there</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">away to pick sites in one and remove in another?
Eg. pick sites at 3 sigma</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">in FoFc and remove if 1.2 sigma in 2FoFc.</font></div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">I thought h-bonding was generously about
2.4-3.6A so why the 1.8 and 3.2</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">defaults? Also if use_hydrogens = True, does
the refinement use h_bond</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">parameters instead of model_peak_dist and
peak_peak_dist parameters, or</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">both? Also what do all of the peak_search
parameters do?</font></div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">And finally does anyone have any recommendations
for progessively changing</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">the ordered_solvent parameters? In CNS we used
to gradually lower the</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">2FoFc peak picking (and deleting) and increase
the bfactor_max for</font></div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">deleting?</font></div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<div style="margin: 0px;"><font
style="font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal;"
face="Arial" size="4">Thanks Mark</font></div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<div
style="margin: 0px; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 13px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 15px;"><br>
</div>
<br>
<pre wrap="">
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