[phenixbb] Confused with ANAISOU in PDB

Partha Chakrabarti ppchak at gmail.com
Tue Oct 9 14:10:51 PDT 2007


Forgot to say, the statistics look nearly as good, just a difference of 1%.

At 1.8A, 55% solvent, 159 water molecules compared to 330 as I got last
time.

Start R-work = 0.2860, R-free = 0.3259
Final R-work = 0.2051, R-free = 0.2563

Thanks for the explanation.

Cheers, Partha


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