<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>Sorry, I should have made it clear.</div><div><br class="webkit-block-placeholder"></div><div>I started a refinement using phenix.refine with riding H in my model. After the refinement, I got the following at the end of the log and the header of the pdb file.</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><div><br class="webkit-block-placeholder"></div><div><br class="webkit-block-placeholder"></div>Using this refined model, I did phenix.pdbtools model.pdb --show-geometry-statistics. And I got the following.</span></span></span></span></span></span></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br class="webkit-block-placeholder"></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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></div></span></div></span>Using this refined model, I did phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0 strategy=none. And I got the following. </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">------------------------------------------------------------------------</font></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 : 0.608 0.003 0.120 12.395 0.003 3.928 2.9651e-02</font></div><div><font class="Apple-style-span" face="Courier">------------------------------------------------------------------------</font></div><div><br class="webkit-block-placeholder"></div></div><div apple-content-edited="true">After removing the H from the refined model, I did phenix.pdbtools model_noH.pdb --show-geometry-statistics. And I got the following.</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><div apple-content-edited="true"><br class="webkit-block-placeholder"></div><div apple-content-edited="true"><br class="webkit-block-placeholder"></div><div apple-content-edited="true">Jianghai</div><div apple-content-edited="true"><br class="webkit-block-placeholder"></div><div apple-content-edited="true"><br class="webkit-block-placeholder"></div><div><div>On Feb 21, 2008, at 8:35 PM, Pavel Afonine wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div bgcolor="#ffffff" text="#000000"> Hi Jianghai,<br> <br> I'm confused about what you're comparing with what. Could you please try this:<br> <br> 1) Take a model;<br> <br> 2) Run phenix.refine with it:<br> <br> % phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0 strategy=none<br> <br> 3) Run phenix.pdbtools with it:<br> <br> % phenix.pdbtools model.pdb --show-geometry-statistics<br> <br> Is the geometry statistics reported by phenix.refine and phenix.pdbtools different? If it is different then there is a problem and to fix it I will need to look at that PDB file.<br> <br> Pavel.<br> <br></div></blockquote></div><br></body></html>