<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div apple-content-edited="true"><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-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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Here are the results.</div><div><br class="webkit-block-placeholder"></div><div>phenix.pdbtools, riding H in the model.</div><div><br class="webkit-block-placeholder"></div><div> |<font class="Apple-style-span" face="Courier">-Geometry statistics---------------------------------------------------------|</font></div><div><font class="Apple-style-span" face="Courier">| Type | Count | Deviation from ideal | Targets | Target (sum) |</font></div><div><font class="Apple-style-span" face="Courier">| | | rmsd max min | | |</font></div><div><font class="Apple-style-span" face="Courier">| bond | 99522 | 0.004 0.085 0.000 | 0.028 | |</font></div><div><font class="Apple-style-span" face="Courier">| angle | 179035 | 0.793 21.106 0.000 | 0.099 | |</font></div><div><font class="Apple-style-span" face="Courier">| chirality | 7686 | 0.126 4.889 0.000 | 0.396 | 0.060 |</font></div><div><font class="Apple-style-span" face="Courier">| planarity | 15814 | 0.004 0.089 0.000 | 0.060 | |</font></div><div><font class="Apple-style-span" face="Courier">| dihedral | 24985 | 15.478 87.363 0.000 | 1.129 | |</font></div><div><font class="Apple-style-span" face="Courier">| nonbonded | 99522 | 3.939 4.900 1.125 | 0.725 | |</font></div><div><font class="Apple-style-span" face="Courier">|-----------------------------------------------------------------------------|</font></div><div><font class="Apple-style-span" face="Courier"><br class="webkit-block-placeholder"></font></div></span></span></span></span></span></span></div></span></div></span>phenix.pdbtools, without H in the model. </div><div apple-content-edited="true"><br class="webkit-block-placeholder"></div><div apple-content-edited="true"><div><font class="Apple-style-span" face="Courier">|-Geometry statistics---------------------------------------------------------|</font></div><div><font class="Apple-style-span" face="Courier">| Type | Count | Deviation from ideal | Targets | Target (sum) |</font></div><div><font class="Apple-style-span" face="Courier">| | | rmsd max min | | |</font></div><div><font class="Apple-style-span" face="Courier">| bond | 51167 | 0.005 0.085 0.000 | 0.054 | |</font></div><div><font class="Apple-style-span" face="Courier">| angle | 69163 | 1.030 21.106 0.000 | 0.194 | |</font></div><div><font class="Apple-style-span" face="Courier">| chirality | 7686 | 0.126 4.889 0.000 | 0.396 | 0.142 |</font></div><div><font class="Apple-style-span" face="Courier">| planarity | 9110 | 0.005 0.089 0.000 | 0.104 | |</font></div><div><font class="Apple-style-span" face="Courier">| dihedral | 18756 | 17.864 87.363 0.000 | 1.504 | |</font></div><div><font class="Apple-style-span" face="Courier">| nonbonded | 51167 | 4.092 4.900 1.434 | 0.639 | |</font></div><div><font class="Apple-style-span" face="Courier">|-----------------------------------------------------------------------------|</font></div><div><br class="webkit-block-placeholder"></div><div>phenix.refine reports at the end of the refinement with riding H.</div><div><br class="webkit-block-placeholder"></div><div><div><font class="Apple-style-span" face="Courier"> stage angl bond chir dihe plan repu geom_target</font></div><div><font class="Apple-style-span" face="Courier"> 0 : 1.394 0.124 0.147 20.782 0.004 3.925 1.1922e+00</font></div><div><font class="Apple-style-span" face="Courier">...</font></div><div><font class="Apple-style-span" face="Courier"> 6_bss: 0.622 0.011 0.120 13.143 0.003 3.822 2.6112e-02</font></div><div><br></div><div><br class="webkit-block-placeholder"></div></div></div><div apple-content-edited="true">They are all different.</div><div apple-content-edited="true"><br class="webkit-block-placeholder"></div><div apple-content-edited="true">Jianghai</div><br><div><div>On Feb 21, 2008, at 6:01 PM, Pavel Afonine wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><blockquote type="cite">Is it possible that phenix.pdbtools ignored the H atoms when <br></blockquote><blockquote type="cite">calculating the geometry statistics?<br></blockquote><blockquote type="cite"><br></blockquote><br>Currently no. But you can easily do it in two steps:<br><br>1) phenix.pdbtools model.pdb remove="element H" <br>output.file_name=model_noH.pdb<br><br>2) phenix.pdbtools model_noH.pdb --show-geometry-statistics<br><br>Pavel.<br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://www.phenix-online.org/mailman/listinfo/phenixbb</blockquote></div><br></body></html>