<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><div>Hi Joe,<br>Below are some notes regarding our ADP restraints. At your resolution the defaults may be too tight.<br>The choice of scattering table shouldn't matter, except for small runtime differences. (You can find some notes here:<br><span><a target="_blank" href="http://cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf">http://cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf</a></span><br>section 4.)<br>Ralf<br><br><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">We use "local sphere restraints".</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> adp_restraints
{</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> iso {</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> sphere_radius = 5.0</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> distance_power = 1.69</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> average_power = 1.03</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"> }</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> }</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">The basic idea is to restrain each adp to the average of all its</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">neighbors within a sphere of a given radius (sphere_radius = 5). The</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">contribution to the refinement target function is:</span><br
style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> (u_i - u_j)**2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 1 / (r_ij ** distance_power) * ----------------------------------</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"> ((u_i + u_j)/2) ** average_power</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">These terms are computed over a double sum: loop over each atom, loop</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">over all neighbors of the atom. I'm not sure anymore how exactly we</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">arrived at
distance_power = 1.69 and average_power = 1.03.</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">You can try different values for distance_power to change the</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">tightness of the restraints as a function of the distance of</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">a pair of atoms. The average_power links the tightness to the</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">absolute value of the adp; average_power=0 turns this feature off.</span><br style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">There are some remarks about this in the "ADP refinement" section in</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">this old newsletter article:</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span> <a target="_blank" href="http://www.phenix-online.org/papers/ccp4_july_2005_afonine.pdf">http://www.phenix-online.org/papers/ccp4_july_2005_afonine.pdf</a></span></span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">The formulas are a bit different (above is current), but the ideas</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">still apply.</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br></div><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><div style="font-family: times new roman,new york,times,serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><b><span style="font-weight: bold;">From:</span></b> Joseph Noel <noel@salk.edu><br><b><span style="font-weight: bold;">To:</span></b> phenixbb@phenix-online.org<br><b><span style="font-weight: bold;">Sent:</span></b> Sun,
December 19, 2010 12:58:43 PM<br><b><span style="font-weight: bold;">Subject:</span></b> [phenixbb] ADP restraints - distance power, average power, etc<br></font><br>
Hi All,<div><br></div><div>I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?</div><div><br></div><div>I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.</div><div><br></div><div>Thanks!</div><div><br></div><div>Joe<br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><div style="word-wrap: break-word;">___________________________________________________________</div><div style="word-wrap: break-word;">Joseph P. Noel, Ph.D.<br>Investigator, Howard Hughes Medical Institute<br>Professor, The Jack H. Skirball Center for Chemical Biology and
Proteomics<br>The Salk Institute for Biological Studies<br>10010 North Torrey Pines Road<br>La Jolla, CA 92037 USA<br><br>Phone: (858) 453-4100 extension 1442<br>Cell: (858) 349-4700<br>Fax: (858) 597-0855<br>E-mail: <a rel="nofollow" ymailto="mailto:noel@salk.edu" target="_blank" href="mailto:noel@salk.edu">noel@salk.edu</a><br><br><span>Web Site (Salk): <a target="_blank" href="http://www.salk.edu/faculty/faculty_details.php?id=37">http://www.salk.edu/faculty/faculty_details.php?id=37</a></span><br><span>Web Site (HHMI): <a target="_blank" href="http://hhmi.org/research/investigators/noel.html">http://hhmi.org/research/investigators/noel.html</a></span><br>___________________________________________________________<br></div></span></span>
</div>
<br></div></div></div></blockquote>
</div></body></html>