https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Command%3A_couplings_make 2026-05-13T18:32:49Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=CYANA_Command:_couplings_make&diff=7337&oldid=prev 2009-08-13T13:46:12Z

<p><span class="autocomment">Description</span></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 15:46, 13 August 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</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>== Description ==</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>== Description ==</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> <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>Makes new scalar coupling constant restraints. Scalar coupling constant restraints are added between atoms selected by the ''first'' and ''second'' atom selections, respectively, provided that the two atoms are separated by three covalent bonds, of which the second must be a rotatable bond. The scalar coupling constant ''value'', its ''tolerance'', relative ''weight'', and the Karplus curve can be set. The command can also be used to simulate scalar coupling constant restraints on the basis of a given structure: If the '''value''' parameter is not given, the scalar coupling constant value of the new restraints will be set to the average value obtained from the selected conformers using the given Karplus curve. Karplus curves must be given as ''A''+''B'''''*cos(d)'''<del style="font-weight: bold; text-decoration: none;">+</del>''C'''''*cos(d)**2''', where ''A'', ''B'' and ''C'' are real numbers, and '''d''' denotes the value of the torsion angle formed by the two scalar coupled atoms.</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>Makes new scalar coupling constant restraints. Scalar coupling constant restraints are added between atoms selected by the ''first'' and ''second'' atom selections, respectively, provided that the two atoms are separated by three covalent bonds, of which the second must be a rotatable bond. The scalar coupling constant ''value'', its ''tolerance'', relative ''weight'', and the Karplus curve can be set. The command can also be used to simulate scalar coupling constant restraints on the basis of a given structure: If the '''value''' parameter is not given, the scalar coupling constant value of the new restraints will be set to the average value obtained from the selected conformers using the given Karplus curve. Karplus curves must be given as ''A<ins style="font-weight: bold; text-decoration: none;">'''</ins>''+<ins style="font-weight: bold; text-decoration: none;">'''</ins>''B'''''*cos(d)<ins style="font-weight: bold; text-decoration: none;">+</ins>'''''C'''''*cos(d)**2''', where ''A'', ''B'' and ''C'' are real numbers, and '''d''' denotes the value of the torsion angle formed by the two scalar coupled atoms.</div></td></tr> </table>

Admin https://cyana.org/w/index.php?title=CYANA_Command:_couplings_make&diff=7335&oldid=prev 2009-08-13T13:45:02Z

<p><span class="autocomment">Description</span></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 15:45, 13 August 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</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>== Description ==</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>== Description ==</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> <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>Makes new scalar coupling constant restraints. Scalar coupling constant restraints are added between atoms selected by the ''first'' and ''second'' atom selections, respectively, provided that the two atoms are separated by three covalent bonds, of which the second must be a rotatable bond. The scalar coupling constant ''value'', its ''tolerance'', relative ''weight'', and the Karplus curve can be set. The command can also be used to simulate scalar coupling constant restraints on the basis of a given structure: If the '''value''' parameter is not given, the scalar coupling constant value of the new restraints will be set to the average value obtained from the selected conformers using the given Karplus curve. Karplus curves must be given as ''A'' + ''B'' <del style="font-weight: bold; text-decoration: none;">* </del>'''cos(d)''' + ''C'' <del style="font-weight: bold; text-decoration: none;">* </del>'''cos(d)**2''', where ''A'', ''B'' and ''C'' are real numbers, and '''d''' denotes the value of the torsion angle formed by the two scalar coupled atoms.</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>Makes new scalar coupling constant restraints. Scalar coupling constant restraints are added between atoms selected by the ''first'' and ''second'' atom selections, respectively, provided that the two atoms are separated by three covalent bonds, of which the second must be a rotatable bond. The scalar coupling constant ''value'', its ''tolerance'', relative ''weight'', and the Karplus curve can be set. The command can also be used to simulate scalar coupling constant restraints on the basis of a given structure: If the '''value''' parameter is not given, the scalar coupling constant value of the new restraints will be set to the average value obtained from the selected conformers using the given Karplus curve. Karplus curves must be given as ''A''+''B'''''<ins style="font-weight: bold; text-decoration: none;">*</ins>cos(d)'''+''C'''''<ins style="font-weight: bold; text-decoration: none;">*</ins>cos(d)**2''', where ''A'', ''B'' and ''C'' are real numbers, and '''d''' denotes the value of the torsion angle formed by the two scalar coupled atoms.</div></td></tr> </table>

Admin https://cyana.org/w/index.php?title=CYANA_Command:_couplings_make&diff=7231&oldid=prev 2009-08-13T09:58:08Z

<p><span class="autocomment">Parameters</span></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 11:58, 13 August 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"></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> <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>; first=''<del style="font-weight: bold; text-decoration: none;">string</del>'': (required)</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>; first=''<ins style="font-weight: bold; text-decoration: none;">[[atom selection]]</ins>'': (required)</div></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>; second=''<del style="font-weight: bold; text-decoration: none;">string</del>'': (required)</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>; second=''<ins style="font-weight: bold; text-decoration: none;">[[atom selection]]</ins>'': (required)</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>; value=&#039;&#039;real&#039;&#039;: (default: 1.0)</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>; value=&#039;&#039;real&#039;&#039;: (default: 1.0)</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>; tolerance=&#039;&#039;real&#039;&#039;: (default: 1.0)</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>; tolerance=&#039;&#039;real&#039;&#039;: (default: 1.0)</div></td></tr> </table>

Masayo https://cyana.org/w/index.php?title=CYANA_Command:_couplings_make&diff=6981&oldid=prev 2009-08-12T12:17:07Z

<p></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 14:17, 12 August 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"></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> <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>; first=''string'' <del style="font-weight: bold; text-decoration: none;">                </del>(required)</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>; first=''string''<ins style="font-weight: bold; text-decoration: none;">: </ins>(required)</div></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>; second=''string'' <del style="font-weight: bold; text-decoration: none;">              </del>(required)</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>; second=''string''<ins style="font-weight: bold; text-decoration: none;">: </ins>(required)</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>; value=&#039;&#039;real&#039;&#039;: (default: 1.0)</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>; value=&#039;&#039;real&#039;&#039;: (default: 1.0)</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>; tolerance=&#039;&#039;real&#039;&#039;: (default: 1.0)</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>; tolerance=&#039;&#039;real&#039;&#039;: (default: 1.0)</div></td></tr> </table>

Admin https://cyana.org/w/index.php?title=CYANA_Command:_couplings_make&diff=6715&oldid=prev 2009-08-06T14:04:10Z

<p></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 16:04, 6 August 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;"></del></div></td><td colspan="2" class="diff-side-added"></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> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l11">Line 11:</td> <td colspan="2" class="diff-lineno">Line 10:</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>== Description ==</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>== Description ==</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> <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;">Add </del>new scalar coupling constant restraints. Scalar coupling constant</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;">Makes </ins>new scalar coupling constant restraints. Scalar coupling constant restraints are added between atoms selected by the ''first'' and ''second'' atom selections, respectively<ins style="font-weight: bold; text-decoration: none;">, provided that the two atoms are separated by three covalent bonds, of which the second must be a rotatable bond</ins>. The scalar coupling constant ''value'', <ins style="font-weight: bold; text-decoration: none;">its </ins>''tolerance'', <ins style="font-weight: bold; text-decoration: none;">relative </ins>''weight'', and <ins style="font-weight: bold; text-decoration: none;">the Karplus curve can be set</ins>. The command can also be used to simulate scalar coupling constant restraints on the basis of a given structure: If the '''value''' parameter is not given, the scalar coupling constant value of the new restraints will be <ins style="font-weight: bold; text-decoration: none;">set </ins>to the average value obtained from the selected conformers using the given Karplus curve. Karplus curves must be <ins style="font-weight: bold; text-decoration: none;">given as ''</ins>A<ins style="font-weight: bold; text-decoration: none;">'' </ins>+ <ins style="font-weight: bold; text-decoration: none;">''</ins>B<ins style="font-weight: bold; text-decoration: none;">'' </ins>* <ins style="font-weight: bold; text-decoration: none;">'''</ins>cos(d)<ins style="font-weight: bold; text-decoration: none;">''' </ins>+ <ins style="font-weight: bold; text-decoration: none;">''</ins>C<ins style="font-weight: bold; text-decoration: none;">'' </ins>* <ins style="font-weight: bold; text-decoration: none;">'''</ins>cos(d)**2<ins style="font-weight: bold; text-decoration: none;">'''</ins>, where <ins style="font-weight: bold; text-decoration: none;">''</ins>A<ins style="font-weight: bold; text-decoration: none;">''</ins>, <ins style="font-weight: bold; text-decoration: none;">''</ins>B<ins style="font-weight: bold; text-decoration: none;">'' </ins>and <ins style="font-weight: bold; text-decoration: none;">''</ins>C<ins style="font-weight: bold; text-decoration: none;">'' </ins>are real numbers, and <ins style="font-weight: bold; text-decoration: none;">'''</ins>d<ins style="font-weight: bold; text-decoration: none;">''' </ins>denotes the value of the torsion angle formed by the two scalar coupled atoms.</div></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>restraints are added between atoms selected by the <del style="font-weight: bold; text-decoration: none;">'</del>''first<del style="font-weight: bold; text-decoration: none;">'</del>'' and <del style="font-weight: bold; text-decoration: none;">'</del>''second''<del style="font-weight: bold; text-decoration: none;">'</del></div></td><td colspan="2" class="diff-side-added"></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>atom selections, respectively. The scalar coupling constant <del style="font-weight: bold; text-decoration: none;">value,</del></div></td><td colspan="2" class="diff-side-added"></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;">its tolerance, relative weight, and Karplus curve parameters are set</del></div></td><td colspan="2" class="diff-side-added"></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;">as given by the '</del>''value<del style="font-weight: bold; text-decoration: none;">'</del>'', <del style="font-weight: bold; text-decoration: none;">'</del>''tolerance<del style="font-weight: bold; text-decoration: none;">'</del>'', <del style="font-weight: bold; text-decoration: none;">'</del>''weight<del style="font-weight: bold; text-decoration: none;">'</del>'', and <del style="font-weight: bold; text-decoration: none;">'''karpluscurve'''</del></div></td><td colspan="2" class="diff-side-added"></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;">parameters</del>.</div></td><td colspan="2" class="diff-side-added"></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 colspan="2" class="diff-side-added"></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>The command can also be used to simulate scalar coupling constant</div></td><td colspan="2" class="diff-side-added"></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>restraints on the basis of a given structure: If the '''value''' parameter</div></td><td colspan="2" class="diff-side-added"></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>is not given, <del style="font-weight: bold; text-decoration: none;">then </del>the scalar coupling constant value of the new</div></td><td colspan="2" class="diff-side-added"></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>restraints will be to the average value obtained from the selected</div></td><td colspan="2" class="diff-side-added"></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>conformers using the given Karplus curve.</div></td><td colspan="2" class="diff-side-added"></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 colspan="2" class="diff-side-added"></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>Karplus curves must be <del style="font-weight: bold; text-decoration: none;">specified in the form </del>A+B*cos(d)+C*cos(d)**2,</div></td><td colspan="2" class="diff-side-added"></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>where A, B and C are real numbers, and d denotes the value of the</div></td><td colspan="2" class="diff-side-added"></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>torsion angle formed by the two scalar coupled atoms.</div></td><td colspan="2" class="diff-side-added"></td></tr> </table>

Admin https://cyana.org/w/index.php?title=CYANA_Command:_couplings_make&diff=5306&oldid=prev 2009-01-29T11:26:54Z

<p>1 revision</p> <p><b>New page</b></p><div><br /> == Parameters ==<br /> <br /> ; first=&#039;&#039;string&#039;&#039; (required)<br /> ; second=&#039;&#039;string&#039;&#039; (required)<br /> ; value=&#039;&#039;real&#039;&#039;: (default: 1.0)<br /> ; tolerance=&#039;&#039;real&#039;&#039;: (default: 1.0)<br /> ; weight=&#039;&#039;real&#039;&#039;: (default: 1.0)<br /> ; karpluscurve=&#039;&#039;string&#039;&#039;: (default: &#039;&#039;none&#039;&#039;)<br /> <br /> == Description ==<br /> <br /> Add new scalar coupling constant restraints. Scalar coupling constant<br /> restraints are added between atoms selected by the &#039;&#039;&#039;first&#039;&#039;&#039; and &#039;&#039;&#039;second&#039;&#039;&#039;<br /> atom selections, respectively. The scalar coupling constant value,<br /> its tolerance, relative weight, and Karplus curve parameters are set<br /> as given by the &#039;&#039;&#039;value&#039;&#039;&#039;, &#039;&#039;&#039;tolerance&#039;&#039;&#039;, &#039;&#039;&#039;weight&#039;&#039;&#039;, and &#039;&#039;&#039;karpluscurve&#039;&#039;&#039;<br /> parameters.<br /> <br /> The command can also be used to simulate scalar coupling constant<br /> restraints on the basis of a given structure: If the &#039;&#039;&#039;value&#039;&#039;&#039; parameter<br /> is not given, then the scalar coupling constant value of the new<br /> restraints will be to the average value obtained from the selected<br /> conformers using the given Karplus curve.<br /> <br /> Karplus curves must be specified in the form A+B*cos(d)+C*cos(d)**2,<br /> where A, B and C are real numbers, and d denotes the value of the<br /> torsion angle formed by the two scalar coupled atoms.</div>

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