<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 Tim,<br><br>If you start from nearly identical copies (due to previous refinement), in the absence of a strong signal from the data, it is expected that the copies remain fairly similar even if you increase the sigma / lower the weight. We just added a new feature to phenix.refine that could be useful to introduce differences between the NCS copies, guided by the model density through a new real-space refinement protocol: strategy=individual_sites_real_space plus real_space_refinement.mode=lockit. At your resolution it is turned on by default. I.e. to try it out all you need to do is get dev-602 or higher and run phenix.refine again. Only trouble, those installers aren't generally visible since there were some minor problems, but watch out for a new one
soon.<br><br>Ralf<br><br><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> Timothy Springer <springer@idi.harvard.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> Tue, December 7, 2010 7:31:44 PM<br><b><span style="font-weight: bold;">Subject:</span></b> [phenixbb] ncs restraints<br></font><br>
Hi, I am using NCS restraints for 4 copies of a molecule at 3.05 �. We are using the standard weights:<div><div> coordinate_sigma = 0.05</div><div> b_factor_weight = 10</div><div>and the 4 molecules look identical. What are suggested values for looser restraints? One of my colleagues said that varying them did not make a difference- ncs was still very strict. Is there a way to make them less strict?</div><div>Thanks,</div><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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: Helvetica; font-size: 12px; 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;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><div style="word-wrap: break-word;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><div style="font-family: Arial;">Timothy A. Springer, Ph.D. </div><div style="font-family: Arial;"><span class="Apple-converted-space"></span></div><div style="font-family: Arial;"><font class="Apple-style-span" face="Helvetica"><font class="Apple-style-span" face="Arial"><br></font></font></div></span></span></span></span></div></span></div></span></div></span></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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