https://cyana.org/w/index.php?action=history&feed=atom&title=Grid_search 2026-05-13T21:51:17Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=Grid_search&diff=3751&oldid=prev 2009-01-28T18:18:39Z

<p>1 revision</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:18, 28 January 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>= <del style="font-weight: bold; text-decoration: none;">grid search </del>=</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>= <ins style="font-weight: bold; text-decoration: none;">grid_search </ins>=</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>        </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>        </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Parameters ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Parameters ==</div></td></tr> </table>

Admin https://cyana.org/w/index.php?title=Grid_search&diff=2949&oldid=prev 2009-01-28T18:12:27Z

<p>1 revision</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:12, 28 January 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">= grid search =</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">      </ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Parameters ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Parameters ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> </table>

Admin https://cyana.org/w/index.php?title=Grid_search&diff=2137&oldid=prev 2009-01-28T17:25:56Z

<p>1 revision</p> <p><b>New page</b></p><div><br /> == Parameters ==<br /> <br /> ; tfcut=&#039;&#039;real&#039;&#039;: (default: 0.0)<br /> ; test <br /> <br /> == Description ==<br /> <br /> This command performs a grid search for the current fragment (as<br /> defined by the most recent &#039;&#039;&#039;grid fragment&#039;&#039;&#039; command). The grid search<br /> will be done over all torsion angles in the fragment and with the<br /> number of steps per torsion angle given by the variable &#039;&#039;&#039;nstep&#039;&#039;&#039;. If<br /> the cutoff value given by the &#039;&#039;&#039;tfcut&#039;&#039;&#039; for the local, fragment-based<br /> target function is positive, then all conformations with a local<br /> target function value below this cutoff will be considered as<br /> allowed. Otherwise, a conformation will be allowed if no single<br /> restraint violation exceeds the corresponding &quot;soft&quot; cutoff values<br /> defined by the variables soft_upl, soft_lol, soft_vdw, soft_aco, and<br /> soft_cco. Other types of restraints, e.g. residual dipolar couplings<br /> or pseudocontact shifts, cannot be used in grid searches.<br /> <br /> To avoid excessive computation times for fragments with many angles<br /> and/or few restraints, the calculation is not started if the expected<br /> number of grid points to be checked (after the evaluation of restraints<br /> that involve a single torsion angle) exceeds the value of the variable<br /> &#039;&#039;&#039;gridpoints&#039;&#039;&#039;. Similarly, a grid search is aborted if the estimated<br /> total computation time in seconds exceeds gridtime seconds. If the<br /> number of grid points to be checked (after evaluation of the restraints<br /> that depend on a single dihedral angle) is larger than Nmax, or if<br /> the estimated computation time for the complete grid search exceeds<br /> tmax seconds, the calculation will be stopped.<br /> <br /> If the &#039;&#039;&#039;test&#039;&#039;&#039; option is set, the grid search will not be started but<br /> the expected number of grid points to be checked (after evaluation<br /> of the restraints that depend on a single dihedral angle) will be<br /> reported.<br /> <br /> The grid search is restricted to angle values that are allowed<br /> according to the standard grid memory, A. The resulting allowed angle<br /> values from the grid search will again be stored in the standard<br /> grid memory.<br /> <br /> Further reading:<br /> <br /> Guntert et al. J. Biomol. NMR 12, 543-548 (1998). Guntert et<br /> al. J. Am. Chem. Soc. 111, 3997-4004 (1989).</div>

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