https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&feed=atom&action=history Spot2pdb - Revision history 2024-03-28T11:04:17Z Revision history for this page on the wiki MediaWiki 1.39.6 https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=4477&oldid=prev Kay: /* Notes */ 2023-03-08T14:31:56Z <p><span dir="auto"><span class="autocomment">Notes</span></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 15:31, 8 March 2023</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l40">Line 40:</td> <td colspan="2" class="diff-lineno">Line 40:</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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information for most detectors.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information for most detectors.  </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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, spot2pdb uses [<del style="font-weight: bold; text-decoration: none;">https://{{SERVERNAME}}/pub/linux_bin/generate_XPARM.XDS </del>XDS.INP as a source of geometry information<del style="font-weight: bold; text-decoration: none;">]</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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, spot2pdb uses [<ins style="font-weight: bold; text-decoration: none;">[</ins>XDS.INP<ins style="font-weight: bold; text-decoration: none;">]] </ins>as a source of geometry information.</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=4476&oldid=prev Kay at 09:25, 8 March 2023 2023-03-08T09:25:32Z <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 10:25, 8 March 2023</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>[https://{{SERVERNAME}}/pub/linux_bin/spot2pdb spot2pdb],[https://{{SERVERNAME}}/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions in reciprocal space.</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;">spot2pdb (</ins>[https://{{SERVERNAME}}/pub/linux_bin/spot2pdb <ins style="font-weight: bold; text-decoration: none;">for Linux], [https://{{SERVERNAME}}/pub/mac_bin/</ins>spot2pdb <ins style="font-weight: bold; text-decoration: none;">for Mac</ins>], [https://{{SERVERNAME}}/pub/sources/spot2pdb.f90 <ins style="font-weight: bold; text-decoration: none;">source</ins>]<ins style="font-weight: bold; text-decoration: none;">) </ins>is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions in reciprocal space.</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"></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>The usage is simple: just run</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>The usage is simple: just run</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=4198&oldid=prev Kay: /* Notes */ 2020-11-18T11:00:01Z <p><span dir="auto"><span class="autocomment">Notes</span></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 12:00, 18 November 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l39">Line 39:</td> <td colspan="2" class="diff-lineno">Line 39:</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"></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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information<del style="font-weight: bold; text-decoration: none;">; earlier versions don&#039;t</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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information <ins style="font-weight: bold; text-decoration: none;">for most detectors</ins>.  </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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, <del style="font-weight: bold; text-decoration: none;">one may use </del>[https://{{SERVERNAME}}/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] <del style="font-weight: bold; text-decoration: none;">for &lt;code&gt;spot2pdb&lt;/code&gt;</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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, <ins style="font-weight: bold; text-decoration: none;">spot2pdb uses </ins>[https://{{SERVERNAME}}/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information].</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=4098&oldid=prev Karsten at 13:24, 24 March 2020 2020-03-24T13:24:50Z <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 14:24, 24 March 2020</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;">ftp</del>://{{SERVERNAME}}/pub/linux_bin/spot2pdb spot2pdb],[<del style="font-weight: bold; text-decoration: none;">ftp</del>://{{SERVERNAME}}/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions in reciprocal space.</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;">https</ins>://{{SERVERNAME}}/pub/linux_bin/spot2pdb spot2pdb],[<ins style="font-weight: bold; text-decoration: none;">https</ins>://{{SERVERNAME}}/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions in reciprocal space.</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"></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>The usage is simple: just run</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>The usage is simple: just run</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l40">Line 40:</td> <td colspan="2" class="diff-lineno">Line 40:</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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information; earlier versions don&#039;t.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information; earlier versions don&#039;t.  </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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, one may use [<del style="font-weight: bold; text-decoration: none;">ftp</del>://{{SERVERNAME}}/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] for &lt;code&gt;spot2pdb&lt;/code&gt;.</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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, one may use [<ins style="font-weight: bold; text-decoration: none;">https</ins>://{{SERVERNAME}}/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] for &lt;code&gt;spot2pdb&lt;/code&gt;.</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</div></td></tr> </table> Karsten https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=4038&oldid=prev Karsten at 16:29, 19 December 2019 2019-12-19T16:29:01Z <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 17:29, 19 December 2019</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>[ftp://<del style="font-weight: bold; text-decoration: none;">turn5.biologie.uni-konstanz.de</del>/pub/linux_bin/spot2pdb spot2pdb],[ftp://<del style="font-weight: bold; text-decoration: none;">turn5.biologie.uni-konstanz.de</del>/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions in reciprocal space.</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>[ftp://<ins style="font-weight: bold; text-decoration: none;">{{SERVERNAME}}</ins>/pub/linux_bin/spot2pdb spot2pdb],[ftp://<ins style="font-weight: bold; text-decoration: none;">{{SERVERNAME}}</ins>/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions in reciprocal space.</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"></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>The usage is simple: just run</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>The usage is simple: just run</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l40">Line 40:</td> <td colspan="2" class="diff-lineno">Line 40:</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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* the mapping used by &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the (unrefined) frame header values, and possibly assumptions (as implemented in &lt;code&gt;iotbx.detectors&lt;/code&gt;) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information; earlier versions don&#039;t.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information; earlier versions don&#039;t.  </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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, one may use [ftp://<del style="font-weight: bold; text-decoration: none;">turn5.biologie.uni-konstanz.de</del>/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] for &lt;code&gt;spot2pdb&lt;/code&gt;.</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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, one may use [ftp://<ins style="font-weight: bold; text-decoration: none;">{{SERVERNAME}}</ins>/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] for &lt;code&gt;spot2pdb&lt;/code&gt;.</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; (Paul Emsley, personal communication).</div></td></tr> </table> Karsten https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=3740&oldid=prev Kay: /* Notes */ 2018-04-28T10:12:50Z <p><span dir="auto"><span class="autocomment">Notes</span></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 11:12, 28 April 2018</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l41">Line 41:</td> <td colspan="2" class="diff-lineno">Line 41:</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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information; earlier versions don&#039;t.  </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>* Since &lt;code&gt;dials.rs_mapper&lt;/code&gt; uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if &lt;code&gt;XDS.INP&lt;/code&gt; also has this item. [[generate_XDS.INP]] versions since 0.82 write &lt;code&gt;XDS.INP&lt;/code&gt; with STARTING_ANGLE information; earlier versions don&#039;t.  </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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, one may use [ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] for &lt;code&gt;spot2pdb&lt;/code&gt;.</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>* if no &lt;code&gt;XPARM.XDS&lt;/code&gt; exists, one may use [ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] for &lt;code&gt;spot2pdb&lt;/code&gt;.</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039;.</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>* &lt;code&gt;coot&lt;/code&gt; connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines<ins style="font-weight: bold; text-decoration: none;">) (Paul Emsley, personal communication</ins>). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be &lt;code&gt;coot&lt;/code&gt;&#039;s &#039;&#039;display objects&#039;&#039; <ins style="font-weight: bold; text-decoration: none;">(Paul Emsley, personal communication)</ins>.</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=3739&oldid=prev Kay at 10:10, 28 April 2018 2018-04-28T10:10:13Z <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 11:10, 28 April 2018</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>[ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/spot2pdb spot2pdb],[ftp://turn5.biologie.uni-konstanz.de/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions.</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>[ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/spot2pdb spot2pdb],[ftp://turn5.biologie.uni-konstanz.de/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions <ins style="font-weight: bold; text-decoration: none;">in reciprocal space</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;"><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"></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>The usage is simple: just run</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>The usage is simple: just run</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=3722&oldid=prev Kay at 08:47, 7 March 2018 2018-03-07T08:47:39Z <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 09:47, 7 March 2018</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>[ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/spot2pdb spot2pdb],[ftp://turn5.biologie.uni-konstanz.de/pub/sources/spot2pdb.f90] is a jiffy that <del style="font-weight: bold; text-decoration: none;">serves to create </del>pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions.</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>[ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/spot2pdb spot2pdb],[ftp://turn5.biologie.uni-konstanz.de/pub/sources/spot2pdb.f90] is a jiffy that <ins style="font-weight: bold; text-decoration: none;">creates </ins>pseudo-PDB files for visualization of reciprocal space, based on &lt;code&gt;SPOT.XDS&lt;/code&gt; and &lt;code&gt;XPARM.XDS&lt;/code&gt;. The &quot;atom&quot; positions in the pseudo-PDB files are actually reflections positions.</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"></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>The usage is simple: just run</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>The usage is simple: just run</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=3721&oldid=prev Kay: /* Notes */ 2018-03-07T08:44:07Z <p><span dir="auto"><span class="autocomment">Notes</span></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 09:44, 7 March 2018</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l33">Line 33:</td> <td colspan="2" class="diff-lineno">Line 33:</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"></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>[[File:wrongrotaxis2.png|400px|thumb|right|another view of result with rotation axis 90° off]]</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>[[File:wrongrotaxis2.png|400px|thumb|right|another view of result with rotation axis 90° off]]</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 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;">&lt;br clear=all></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;"><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"></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>== Notes ==</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>== Notes ==</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/xds/index.php?title=Spot2pdb&diff=3720&oldid=prev Kay: /* Examples */ 2018-03-07T08:43:24Z <p><span dir="auto"><span class="autocomment">Examples</span></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 09:43, 7 March 2018</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l20">Line 20:</td> <td colspan="2" class="diff-lineno">Line 20:</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"></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>== Examples ==</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>== Examples ==</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>[[File:insu6A.png]]</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>[[File:insu6A.png<ins style="font-weight: bold; text-decoration: none;">|400px|thumb|left|Indexed spot positions are yellow, un-indexed ones red.</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;"><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;">&#039;&#039;&#039;Indexed </del>spot positions <del style="font-weight: bold; text-decoration: none;">are yellow</del>, <del style="font-weight: bold; text-decoration: none;">un-indexed ones red</del>.<del style="font-weight: bold; text-decoration: none;">&#039;&#039;&#039;</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;">[[File:insu6AplusED.png|400px|thumb|right|Same, but with pseudo electron density. The offset between </ins>spot positions <ins style="font-weight: bold; text-decoration: none;">and electron density is due to a slight error in the header values of ORGX</ins>, <ins style="font-weight: bold; text-decoration: none;">ORGY (see [[spot2pdb#Notes|Notes]] below)</ins>.<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;"><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;">[[File</del>:<del style="font-weight: bold; text-decoration: none;">insu6AplusED.png]]</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;">&lt;br clear=all&gt;Examples with wrong ROTATION_AXIS</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;"><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;">&#039;&#039;&#039;Same, but </del>with <del style="font-weight: bold; text-decoration: none;">pseudo electron density</del>. <del style="font-weight: bold; text-decoration: none;">The offset between spot positions and electron density </del>is <del style="font-weight: bold; text-decoration: none;">due to a slight error in the header values </del>of <del style="font-weight: bold; text-decoration: none;">ORGX, ORGY (see </del>[[<del style="font-weight: bold; text-decoration: none;">spot2pdb#Notes</del>|<del style="font-weight: bold; text-decoration: none;">Notes</del>]] <del style="font-weight: bold; text-decoration: none;">below).&#039;&#039;&#039;</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;">[[File:backwardsrotaxis.png|400px|thumb|left|ROTATION_AXIS is -1 0 0 instead of 1 0 0]]</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> </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;">[[File:backwardsrotaxis2.png|400px|thumb|right|another view of result </ins>with <ins style="font-weight: bold; text-decoration: none;">rotation axis backwards]]</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> </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;">[[File:wrongrotaxis</ins>.<ins style="font-weight: bold; text-decoration: none;">png|400px|thumb|left|ROTATION_AXIS </ins>is <ins style="font-weight: bold; text-decoration: none;">0 1 0 instead </ins>of <ins style="font-weight: bold; text-decoration: none;">1 0 0]]</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> </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;">File:wrongrotaxis2.png</ins>|<ins style="font-weight: bold; text-decoration: none;">400px|thumb|right|another view of result with rotation axis 90° off</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;"><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"></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>== Notes ==</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>== Notes ==</div></td></tr> </table> Kay