I ran the same commands with the build dev-833.<br>Below are the results. <br>These parameters are obtained by running phenix.ramalyze, cbetdev, and clashscore.<br>
I am almost done repeating fix-rotamers run. First time it gave a way
worse validation results then before running phenix without
fix_rotamers=true. <br>
I don't understand what I am doing wrong in the runs and would appreciate your help!<br>
<br>
Thanks,<br>
Tanya<br><br><br>
<p class="MsoNormalCxSpFirst" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">I used phenix-dev-833 to test the
riding hydrogens refinement at 3.6A.</span></p>
<p class="MsoNormalCxSpLast" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">I ran two indentical commands:</span></p>
<p class="MsoPlainText" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">Command line arguments: "model.pdb"
"data.mtz" "main.ncs=true"
"ncs.find_automatically=false" "ncs_groups.params" "refinement.input.xray_data.high_resolution=3.6"
"mgadpbef.cif"
"refinement.ncs.excessive_distance_limit=None"
"strategy=individual_sites+individual_sites_real_space+group_adp+occupancies"</span></p>
<p class="MsoNormalCxSpFirst" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";"><span style="">�</span>with the only difference in the input files �
ncs.params and model.pdb</span></p>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">Model pdb contained the model
identical to the control run but with added H atoms. I have not add H to the
ADP molecules since I did not know how to write a correct CIF file for it. NCS
definitions were changed by addition of �and not (element H)� to each line. It
was done to exclude H from the NCS groups.</span></p>
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<p class="MsoNormalCxSpMiddle" style="margin-bottom: 0.0001pt; text-align: justify;"><u><span style="font-size: 12pt; font-family: "Arial","sans-serif";">no hydrogens</span></u></p>
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<td style="width: 239.4pt; border-width: 1pt 1pt 1pt medium; border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; padding: 0in 5.4pt;" valign="top" width="319">
<p class="MsoNormalCxSpMiddle" style="margin-bottom: 0.0001pt; text-align: justify;"><u><span style="font-size: 12pt; font-family: "Arial","sans-serif";">with hydrogens</span></u><span style="font-size: 12pt; font-family: "Arial","sans-serif";"></span></p>
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<p class="MsoPlainTextCxSpFirst" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";"># Date 2011-07-29
Time 19:09:58 EDT -0400 (1311980998.46 s)</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">wall clock time:
2646.75 s</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">�</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">Start R-work =
0.2891, R-free = 0.3267</span></p>
<p class="MsoPlainTextCxSpLast" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">Final R-work =
0.2868, R-free = <span style="background: none repeat scroll 0% 0% yellow;">0.3304</span></span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">�</span></p>
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<p class="MsoPlainTextCxSpFirst" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";"># Date 2011-07-29
Time 20:14:20 EDT -0400 (1311984860.16 s)</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">wall clock time:
6517.60 s</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">�</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">Start R-work =
0.2910, R-free = 0.3273</span></p>
<p class="MsoPlainTextCxSpLast" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">Final R-work =
0.2720, R-free = <span style="background: none repeat scroll 0% 0% yellow;">0.3353</span></span></p>
<p class="MsoNormalCxSpFirst" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">�</span></p>
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<p class="MsoPlainText" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">clashscore <span style="background: none repeat scroll 0% 0% yellow;">31.77</span></span></p>
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<td style="width: 239.4pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0in 5.4pt;" valign="top" width="319">
<p class="MsoNormalCxSpFirst" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">clashscore <span style="background: none repeat scroll 0% 0% yellow;">96.12</span></span></p>
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<p class="MsoPlainText" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">cbeta <span style="background: none repeat scroll 0% 0% yellow;">0</span></span></p>
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<td style="width: 239.4pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0in 5.4pt;" valign="top" width="319">
<p class="MsoNormalCxSpFirst" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">cbeta <span style="background: none repeat scroll 0% 0% yellow;">151</span></span></p>
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<td style="width: 239.4pt; border-width: medium 1pt 1pt; border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; padding: 0in 5.4pt; background-color: rgb(255, 255, 255);" valign="top" width="319">
<p class="MsoPlainText" style="text-align: justify;"><span style="font-family: "Courier New"; background-image: none; background-repeat: repeat; background-attachment: scroll; background-position: 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-size: auto auto;">rama 12.62</span><span style="font-family: "Courier New";">% outliers</span><span style="font-size: 12pt; font-family: "Arial","sans-serif";"></span></p>
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<td style="width: 239.4pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0in 5.4pt;" valign="top" width="319">
<p class="MsoNormalCxSpFirst" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-size: 10.5pt; font-family: "Courier New"; background: none repeat scroll 0% 0% rgb(255, 255, 255);">rama 19.67</span><span style="font-size: 10.5pt; font-family: "Courier New"; background-color: rgb(255, 255, 255);">% outliers</span><span style="font-size: 12pt; font-family: "Arial","sans-serif";"></span></p>
</td>
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</tbody></table>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">�</span></p>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">Interestingly in previous release
version the same refinement runs produced:</span></p>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span style="font-size: 12pt; font-family: "Arial","sans-serif";">without H clashscore = 77.580195/cbeta
=8</span></p>
<span style="font-size: 12pt; font-family: "Arial","sans-serif";">with H clashscore = 119.729960/cbeta=330</span><br><br><br>