<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Mark,<div><br></div><div>I would be quite interested in opinions about the usage and assignment of hydrogens in the riding position for refinement too, especially at low resolution of around 4 A. How important are they for obtaining reasonable geometry at that resolution?</div><div><br></div><div>From what I could see in the phenix manual hydrogens should<span class="Apple-style-span" style="font-family: verdana, helvetica, arial, sans-serif; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> should not be included into NCS or TLS groups and are automatically excluded from them. </span></font></span></div><div><span class="Apple-style-span" style="font-family: verdana, helvetica, arial, sans-serif; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font></span></div><div><font class="Apple-style-span" face="verdana, helvetica, arial, sans-serif"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; ">Cheers,</span></font></div><div><font class="Apple-style-span" face="verdana, helvetica, arial, sans-serif"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><br></span></font></div><div><font class="Apple-style-span" face="verdana, helvetica, arial, sans-serif"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; ">Florian</span></font></div><div><font class="Apple-style-span" face="verdana, helvetica, arial, sans-serif"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><br></span></font></div><div><div>On Oct 5, 2010, at 9:32 PM, Mayer, Mark (NIH/NICHD) [E] wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Nat,<br><br>After the long discussion, mostly on CCP4BB, about riding H,<br>which covered different H-bond lengths, it would be really<br>good if the GUI and other Phenix documentation explained<br>exactly how this is handled. <br><br>I think using riding H as a geometry restraint during refinement<br>should be standard practice, but I think 'interpreting' those H atoms<br>in all but the very highest resolution X-ray structures is probably<br>not good. <br><br>Mark<br>________________________________________<br>From: Nathaniel Echols [<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>]<br>Sent: Tuesday, October 05, 2010 3:56 PM<br>To: PHENIX user mailing list<br>Subject: Re: [phenixbb] Problem with Molprobity analysis in phenix 1.6.4<br><br>On Tue, Oct 5, 2010 at 11:53 AM, Mark A Saper <<a href="mailto:saper@umich.edu">saper@umich.edu</a>> wrote:<br><blockquote type="cite">If I take my well-refined structure as output by phenix (.pdb) and use it<br></blockquote><blockquote type="cite">directly on the Molprobity web site, the clash score is much lower: 2.75 for<br></blockquote><blockquote type="cite">39 total bumps. Many of these involve residues or waters with high B<br></blockquote><blockquote type="cite">factors.<br></blockquote><blockquote type="cite">If I first remove all hydrogens from the phenix-refined .pdb file with a<br></blockquote><blockquote type="cite">text editor, and upload it to the Molprobity web site, then add hydrogens,<br></blockquote><blockquote type="cite">and then calculate clash score, the score is now 8.69 or 123 bumps for 14150<br></blockquote><blockquote type="cite">atoms. This is *identical* to what phenix calculates. Therefore, why<br></blockquote><blockquote type="cite">doesn't phenix feed the refined coordinates directly into the Molprobity<br></blockquote><blockquote type="cite">(probe) calculations? Has this change been made in one of the nightly<br></blockquote><blockquote type="cite">builds?<br></blockquote><br>There is a discrepancy in hydrogen bond lengths in Reduce versus the<br>monomer library - I believe Reduce is using the distance to the center<br>of the nucleus instead of the center of the electron cloud.<br>phenix.refine will regularize the hydrogen geometry before refining<br>the non-hydrogen coordinates, so it is correcting the bond lengths to<br>be appropriate for X-ray refinement. It looks like they're getting<br>stripped off and replaced when we run the clashscore calculations, so<br>you end up with the longer bonds and thus more clashes. I think the<br>consensus among the group was that these are more appropriate for<br>interpreting (instead of refining) the model, but I'll double-check<br>this with everyone. The GUI could at least be more explicit about how<br>the calculations are done, however.<br><br>(By the way, a clashscore of 8.69 is pretty decent anyway.)<br><br>-Nat<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br>_______________________________________________<br>phenixbb mailing list<br>phenixbb@phenix-online.org<br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; 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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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------------------</div><div>Florian Schmitzberger</div><div>Biological Chemistry and Molecular Pharmacology</div><div>Harvard Medical School</div><div>250 Longwood Avenue, SGM 130 </div><div>Boston, MA 02115, US</div><div>Tel: 001 617 432 5602</div><div><br></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"> </div><br></body></html>