https://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&feed=atom&action=historyTop Ten Tips - Revision history2024-03-28T22:23:42ZRevision history for this page on the wikiMediaWiki 1.31.8https://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=2409&oldid=prevRandy: Add links and citations for sequence alignment tools2017-09-02T13:36:18Z<p>Add links and citations for sequence alignment tools</p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search separately for domains of flexible proteins'''<br/>If there are domain movements, the individual domains will be better models giving a clearer signal than the whole protein.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search separately for domains of flexible proteins'''<br/>If there are domain movements, the individual domains will be better models giving a clearer signal than the whole protein.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Use sculptor'''<br/>For low sequence identity (<30%) or other difficult cases for which a default Phaser run fails, use sculptor to trim off loops that don't align and to prune back non-identical side chains.  Test models derived with all the protocols.  The best results are obtained with accurate sequence alignments, which can be obtained for instance from HHpred, PROMALS3D or FFAS.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Use sculptor'''<br/>For low sequence identity (<30%) or other difficult cases for which a default Phaser run fails, use sculptor to trim off loops that don't align and to prune back non-identical side chains.  Test models derived with all the protocols.  The best results are obtained with accurate sequence alignments, which can be obtained for instance from <ins class="diffchange diffchange-inline">[https://toolkit.tuebingen.mpg.de/#/tools/hhpred </ins>HHpred<ins class="diffchange diffchange-inline">] ([https://www.ncbi.nlm.nih.gov/pubmed/27131380 citation])</ins>, <ins class="diffchange diffchange-inline">[http://prodata.swmed.edu/promals3d/promals3d.php </ins>PROMALS3D<ins class="diffchange diffchange-inline">] ([https://www.ncbi.nlm.nih.gov/pubmed/18287115 citation]) </ins>or <ins class="diffchange diffchange-inline">[http://ffas.sanfordburnham.org/ffas-cgi/cgi/ffas.pl </ins>FFAS<ins class="diffchange diffchange-inline">] ([https://www.ncbi.nlm.nih.gov/pubmed/15980471 citation])</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use ensembler'''<br/>Molecular replacement can be difficult when the sequence identity is low, but then you probably have several choices of model with similarly low sequence identity.  Construct an ensemble by using the multiple structure alignment in ensembler, and try the option to trim poorly-conserved regions to produce a conserved core.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use ensembler'''<br/>Molecular replacement can be difficult when the sequence identity is low, but then you probably have several choices of model with similarly low sequence identity.  Construct an ensemble by using the multiple structure alignment in ensembler, and try the option to trim poorly-conserved regions to produce a conserved core.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this will only be improved slightly by the most sophisticated modelling algorithms. The identity you enter should thus be the same as  that of the original sequence of your model.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this will only be improved slightly by the most sophisticated modelling algorithms. The identity you enter should thus be the same as  that of the original sequence of your model.</div></td></tr>
</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=2147&oldid=prevAirlie at 14:07, 19 January 20152015-01-19T14:07:50Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:07, 19 January 2015</td>
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<tr><td class='diff-marker'>−</td><td style="color: #222; 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>Here are our Top Ten Tips for MR, SAD and MR-SAD phasing in Phaser</div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">;</ins>Here are our Top Ten Tips for MR, SAD and MR-SAD phasing in Phaser</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td></tr>
</table>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=2090&oldid=prevAirlie at 11:45, 13 January 20152015-01-13T11:45:42Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:45, 13 January 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
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<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">===Molecular replacement===</del></div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">Here are our Top Ten Tips for MR, SAD and MR-SAD phasing in Phaser</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this will only be improved slightly by the most sophisticated modelling algorithms. The identity you enter should thus be the same as  that of the original sequence of your model.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this will only be improved slightly by the most sophisticated modelling algorithms. The identity you enter should thus be the same as  that of the original sequence of your model.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''You may need to change the packing criteria'''<br/>Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In recent versions of Phaser this is less of a problem than it used to be, but it is still worth being aware of.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''You may need to change the packing criteria'''<br/>Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In recent versions of Phaser this is less of a problem than it used to be, but it is still worth being aware of.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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;">===SAD phasing===</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for different anomalous scatterers concurrently'''<br/>If there are multiple types of anomalous scatterer present in your crystal (such as Fe and S), Phaser will get better results by distinguishing between them. If there is a good signal, the correct hand can be identified as the one with the highest LLG score.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for different anomalous scatterers concurrently'''<br/>If there are multiple types of anomalous scatterer present in your crystal (such as Fe and S), Phaser will get better results by distinguishing between them. If there is a good signal, the correct hand can be identified as the one with the highest LLG score.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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;">===Both===</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the MR-SAD mode'''<br/>After molecular replacement, if there is significant anomalous signal in your data, use the MR-SAD mode to identify the anomalous scatterers and improve the phase information.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the MR-SAD mode'''<br/>After molecular replacement, if there is significant anomalous signal in your data, use the MR-SAD mode to identify the anomalous scatterers and improve the phase information.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Install the latest version of Phaser'''<br/>We work hard so you don't have to!</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Install the latest version of Phaser'''<br/>We work hard so you don't have to!</div></td></tr>
</table>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=1259&oldid=prevAirlie at 13:11, 24 April 20122012-04-24T13:11:06Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:11, 24 April 2012</td>
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<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">'''</del>Molecular replacement<del class="diffchange diffchange-inline">'''<br/></del></div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">===</ins>Molecular replacement<ins class="diffchange diffchange-inline">===</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the asymmetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 7:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this will only be improved slightly by the most sophisticated modelling algorithms. The identity you enter should thus be the same as  that of the original sequence of your model.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this will only be improved slightly by the most sophisticated modelling algorithms. The identity you enter should thus be the same as  that of the original sequence of your model.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''You may need to change the packing criteria'''<br/>Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In recent versions of Phaser this is less of a problem than it used to be, but it is still worth being aware of.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''You may need to change the packing criteria'''<br/>Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In recent versions of Phaser this is less of a problem than it used to be, but it is still worth being aware of.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline"><br/>'''</del>SAD phasing<del class="diffchange diffchange-inline">'''<br/></del></div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">===</ins>SAD phasing<ins class="diffchange diffchange-inline">===</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for different anomalous scatterers concurrently'''<br/>If there are multiple types of anomalous scatterer present in your crystal (such as Fe and S), Phaser will get better results by distinguishing between them. If there is a good signal, the correct hand can be identified as the one with the highest LLG score.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Search for different anomalous scatterers concurrently'''<br/>If there are multiple types of anomalous scatterer present in your crystal (such as Fe and S), Phaser will get better results by distinguishing between them. If there is a good signal, the correct hand can be identified as the one with the highest LLG score.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline"><br/>'''</del>Both<del class="diffchange diffchange-inline">'''<br/></del></div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">===</ins>Both<ins class="diffchange diffchange-inline">===</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the MR-SAD mode'''<br/>After molecular replacement, if there is significant anomalous signal in your data, use the MR-SAD mode to identify the anomalous scatterers and improve the phase information.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the MR-SAD mode'''<br/>After molecular replacement, if there is significant anomalous signal in your data, use the MR-SAD mode to identify the anomalous scatterers and improve the phase information.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Install the latest version of Phaser'''<br/>We work hard so you don't have to!</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Install the latest version of Phaser'''<br/>We work hard so you don't have to!</div></td></tr>
</table>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=1226&oldid=prevRandy: Update tips, add some for SAD and both2012-04-24T10:38:43Z<p>Update tips, add some for SAD and both</p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 10:38, 24 April 2012</td>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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;">'''Molecular replacement'''<br/></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the <del class="diffchange diffchange-inline">asymetric </del>unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Search for components concurrently'''<br/>You should search for all components of the <ins class="diffchange diffchange-inline">asymmetric </ins>unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Search <del class="diffchange diffchange-inline">order is important</del>'''<br/><del class="diffchange diffchange-inline">The order in which you search for multiple solutions can affect your success in finding a solution. Components that account for the highest proportion of the scattering (highest completeness, highest sequence identity, and lowest B-factors) should be searched for first. </del>If <del class="diffchange diffchange-inline">you </del>are <del class="diffchange diffchange-inline">not sure which order is best</del>, <del class="diffchange diffchange-inline">you can use </del>the <del class="diffchange diffchange-inline">PERMUTATIONS ON keyword, which </del>will <del class="diffchange diffchange-inline">search with all permutations of your input search components, but if you have a large number of different components </del>be <del class="diffchange diffchange-inline">aware that this search will take </del>a <del class="diffchange diffchange-inline">long time, especially if the </del>signal <del class="diffchange diffchange-inline">from one of </del>the <del class="diffchange diffchange-inline">components is not clear</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Search <ins class="diffchange diffchange-inline">separately for domains of flexible proteins</ins>'''<br/>If <ins class="diffchange diffchange-inline">there </ins>are <ins class="diffchange diffchange-inline">domain movements</ins>, the <ins class="diffchange diffchange-inline">individual domains </ins>will be <ins class="diffchange diffchange-inline">better models giving </ins>a <ins class="diffchange diffchange-inline">clearer </ins>signal <ins class="diffchange diffchange-inline">than </ins>the <ins class="diffchange diffchange-inline">whole protein</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">You may need to change the packing criteria</del>'''<br/><del class="diffchange diffchange-inline">Sometimes valid solutions are excluded because the number clashes is higher than the allowed </del>default <del class="diffchange diffchange-inline">number. Look in the log and summary files to see how many high Z-score solutions </del>Phaser <del class="diffchange diffchange-inline">is rejecting because of clashes</del>, and <del class="diffchange diffchange-inline">how many clashes there are in each case. In versions 1.x the default packing criterion is very strict </del>- <del class="diffchange diffchange-inline">*no* clashes between C-alpha atoms are allowed</del>. <del class="diffchange diffchange-inline">In versions 2.x the default packing criterion is relaxed so that the solutions </del>with the <del class="diffchange diffchange-inline">lowest number of clashes </del>are <del class="diffchange diffchange-inline">allowed</del>, <del class="diffchange diffchange-inline">provided that number is 10 </del>or <del class="diffchange diffchange-inline">less</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">Use sculptor</ins>'''<br/><ins class="diffchange diffchange-inline">For low sequence identity (<30%) or other difficult cases for which a </ins>default Phaser <ins class="diffchange diffchange-inline">run fails</ins>, <ins class="diffchange diffchange-inline">use sculptor to trim off loops that don't align </ins>and <ins class="diffchange diffchange-inline">to prune back non</ins>-<ins class="diffchange diffchange-inline">identical side chains</ins>. <ins class="diffchange diffchange-inline"> Test models derived </ins>with <ins class="diffchange diffchange-inline">all </ins>the <ins class="diffchange diffchange-inline">protocols.  The best results </ins>are <ins class="diffchange diffchange-inline">obtained with accurate sequence alignments, which can be obtained for instance from HHpred</ins>, <ins class="diffchange diffchange-inline">PROMALS3D </ins>or <ins class="diffchange diffchange-inline">FFAS</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">You may need to change the peak selection criteria</del>'''<br/><del class="diffchange diffchange-inline">By default</del>, <del class="diffchange diffchange-inline">Phaser selects peaks that are between 75% and 100% of the difference between the top peak and the mean of the search for inclusion in the next round of the search (rotation or translation function). If </del>you have <del class="diffchange diffchange-inline">many components in the asymmetric unit, the signal from the first rotation search may be very </del>low<del class="diffchange diffchange-inline">, and you may need to decrease the cut-off for the rotation search to 70% or 65% </del>using <del class="diffchange diffchange-inline">FINAL ROT SELECT PERCENT 65.</del></div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">Use ensembler</ins>'''<br/><ins class="diffchange diffchange-inline">Molecular replacement can be difficult when the sequence identity is low</ins>, <ins class="diffchange diffchange-inline">but then </ins>you <ins class="diffchange diffchange-inline">probably </ins>have <ins class="diffchange diffchange-inline">several choices of model with similarly </ins>low <ins class="diffchange diffchange-inline">sequence identity.  Construct an ensemble by </ins>using the <ins class="diffchange diffchange-inline">multiple structure alignment </ins>in <ins class="diffchange diffchange-inline">ensembler</ins>, and <ins class="diffchange diffchange-inline">try </ins>the <ins class="diffchange diffchange-inline">option to trim poorly-conserved regions to produce a conserved core</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#'''Beware </del>the <del class="diffchange diffchange-inline">automated space group determination'''<br/>The space group is determined from the signal in the translation function search for the *first* model. If you have many components </del>in <del class="diffchange diffchange-inline">the asymmetric unit, the signal from this search may be poor</del>, and <del class="diffchange diffchange-inline">you should perform and exhaustive search in all </del>the <del class="diffchange diffchange-inline">alternative space groups</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this <ins class="diffchange diffchange-inline">will only be </ins>improved <ins class="diffchange diffchange-inline">slightly </ins>by the <ins class="diffchange diffchange-inline">most sophisticated modelling algorithms</ins>. The identity you enter should thus be the same as <ins class="diffchange diffchange-inline"> </ins>that of the original sequence of your model.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this <del class="diffchange diffchange-inline">has *not* been </del>improved by the <del class="diffchange diffchange-inline">mutation (in fact, it has probably been made worse!)</del>. The identity you enter should thus be the same as <del class="diffchange diffchange-inline">(or less!) than </del>that of the original sequence of your model.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">You may need to change </ins>the <ins class="diffchange diffchange-inline">packing criteria</ins>'''<br/><ins class="diffchange diffchange-inline">Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look </ins>in the <ins class="diffchange diffchange-inline">log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each </ins>case<ins class="diffchange diffchange-inline">. In recent versions </ins>of <ins class="diffchange diffchange-inline">Phaser this is less of a </ins>problem <ins class="diffchange diffchange-inline">than it used to </ins>be, <ins class="diffchange diffchange-inline">but it </ins>is <ins class="diffchange diffchange-inline">still worth being aware of</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">Reduce </del>the <del class="diffchange diffchange-inline">resolution if you can't find second and subsequent components</del>'''<br/><del class="diffchange diffchange-inline">The current algorithms have a limitation </del>in <del class="diffchange diffchange-inline">that they do not handle </del>the case <del class="diffchange diffchange-inline">where components </del>of <del class="diffchange diffchange-inline">the asymmetric unit have greatly varying B-factors. This </del>problem <del class="diffchange diffchange-inline">can </del>be <del class="diffchange diffchange-inline">worked around by cutting the resolution to about 4 Angstroms</del>, <del class="diffchange diffchange-inline">where the B-factor difference </del>is <del class="diffchange diffchange-inline">less significant</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline"><br/>'''SAD phasing'''<br/></ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">Look at the FAQ list</del>'''<br/>If Phaser <del class="diffchange diffchange-inline">produces </del>a <del class="diffchange diffchange-inline">strange error</del>, <del class="diffchange diffchange-inline">or you don</del>'<del class="diffchange diffchange-inline">t understand some of </del>the <del class="diffchange diffchange-inline">output</del>, <del class="diffchange diffchange-inline">chances are that you are not </del>the <del class="diffchange diffchange-inline">first person </del>to <del class="diffchange diffchange-inline">want know what it all means. If we get asked a question three times it usually goes on </del>the <del class="diffchange diffchange-inline">FAQ list</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">Search for different anomalous scatterers concurrently</ins>'''<br/>If <ins class="diffchange diffchange-inline">there are multiple types of anomalous scatterer present in your crystal (such as Fe and S), </ins>Phaser <ins class="diffchange diffchange-inline">will get better results by distinguishing between them. If there is </ins>a <ins class="diffchange diffchange-inline">good signal</ins>, <ins class="diffchange diffchange-inline">the correct hand can be identified as the one with the highest LLG score.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline"><br/>'''Both'''<br/></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">#''</ins>'<ins class="diffchange diffchange-inline">Use </ins>the <ins class="diffchange diffchange-inline">MR-SAD mode'''<br/>After molecular replacement</ins>, <ins class="diffchange diffchange-inline">if there is significant anomalous signal in your data, use </ins>the <ins class="diffchange diffchange-inline">MR-SAD mode </ins>to <ins class="diffchange diffchange-inline">identify the anomalous scatterers and improve </ins>the <ins class="diffchange diffchange-inline">phase information</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Install the latest version of Phaser'''<br/>We work hard so you don't have to!</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>#'''Install the latest version of Phaser'''<br/>We work hard so you don't have to!</div></td></tr>
</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=414&oldid=prevWikiSysop: remove #: formatting (unstable) with <br/> line breaks2009-07-14T13:11:51Z<p>remove #: formatting (unstable) with <br/> line breaks</p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:11, 14 July 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
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<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Use the automated search'''</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Use the automated search'''<ins class="diffchange diffchange-inline"><br/></ins>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Search for components concurrently'''<ins class="diffchange diffchange-inline"><br/></ins>You should search for all components of the asymetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Search for components concurrently'''</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Search order is important'''<ins class="diffchange diffchange-inline"><br/></ins>The order in which you search for multiple solutions can affect your success in finding a solution. Components that account for the highest proportion of the scattering (highest completeness, highest sequence identity, and lowest B-factors) should be searched for first. If you are not sure which order is best, you can use the PERMUTATIONS ON keyword, which will search with all permutations of your input search components, but if you have a large number of different components be aware that this search will take a long time, especially if the signal from one of the components is not clear.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>You should search for all components of the asymetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''You may need to change the packing criteria'''<ins class="diffchange diffchange-inline"><br/></ins>Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In versions 1.x the default packing criterion is very strict - *no* clashes between C-alpha atoms are allowed. In versions 2.x the default packing criterion is relaxed so that the solutions with the lowest number of clashes are allowed, provided that number is 10 or less.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Search order is important'''</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''You may need to change the peak selection criteria'''<ins class="diffchange diffchange-inline"><br/></ins>By default, Phaser selects peaks that are between 75% and 100% of the difference between the top peak and the mean of the search for inclusion in the next round of the search (rotation or translation function). If you have many components in the asymmetric unit, the signal from the first rotation search may be very low, and you may need to decrease the cut-off for the rotation search to 70% or 65% using FINAL ROT SELECT PERCENT 65.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>The order in which you search for multiple solutions can affect your success in finding a solution. Components that account for the highest proportion of the scattering (highest completeness, highest sequence identity, and lowest B-factors) should be searched for first. If you are not sure which order is best, you can use the PERMUTATIONS ON keyword, which will search with all permutations of your input search components, but if you have a large number of different components be aware that this search will take a long time, especially if the signal from one of the components is not clear.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Beware the automated space group determination'''<ins class="diffchange diffchange-inline"><br/></ins>The space group is determined from the signal in the translation function search for the *first* model. If you have many components in the asymmetric unit, the signal from this search may be poor, and you should perform and exhaustive search in all the alternative space groups.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''You may need to change the packing criteria'''</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Homology models do not have 100% identity'''<ins class="diffchange diffchange-inline"><br/></ins>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this has *not* been improved by the mutation (in fact, it has probably been made worse!). The identity you enter should thus be the same as (or less!) than that of the original sequence of your model.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In versions 1.x the default packing criterion is very strict - *no* clashes between C-alpha atoms are allowed. In versions 2.x the default packing criterion is relaxed so that the solutions with the lowest number of clashes are allowed, provided that number is 10 or less.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Reduce the resolution if you can't find second and subsequent components'''<ins class="diffchange diffchange-inline"><br/></ins>The current algorithms have a limitation in that they do not handle the case where components of the asymmetric unit have greatly varying B-factors. This problem can be worked around by cutting the resolution to about 4 Angstroms, where the B-factor difference is less significant.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''You may need to change the peak selection criteria'''</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Look at the FAQ list'''<ins class="diffchange diffchange-inline"><br/></ins>If Phaser produces a strange error, or you don't understand some of the output, chances are that you are not the first person to want know what it all means. If we get asked a question three times it usually goes on the FAQ list.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>By default, Phaser selects peaks that are between 75% and 100% of the difference between the top peak and the mean of the search for inclusion in the next round of the search (rotation or translation function). If you have many components in the asymmetric unit, the signal from the first rotation search may be very low, and you may need to decrease the cut-off for the rotation search to 70% or 65% using FINAL ROT SELECT PERCENT 65.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>#'''Install the latest version of Phaser'''<ins class="diffchange diffchange-inline"><br/></ins>We work hard so you don't have to!</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Beware the automated space group determination'''</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>The space group is determined from the signal in the translation function search for the *first* model. If you have many components in the asymmetric unit, the signal from this search may be poor, and you should perform and exhaustive search in all the alternative space groups.</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Homology models do not have 100% identity'''</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this has *not* been improved by the mutation (in fact, it has probably been made worse!). The identity you enter should thus be the same as (or less!) than that of the original sequence of your model.</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Reduce the resolution if you can't find second and subsequent components'''</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>The current algorithms have a limitation in that they do not handle the case where components of the asymmetric unit have greatly varying B-factors. This problem can be worked around by cutting the resolution to about 4 Angstroms, where the B-factor difference is less significant.</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Look at the FAQ list'''</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>If Phaser produces a strange error, or you don't understand some of the output, chances are that you are not the first person to want know what it all means. If we get asked a question three times it usually goes on the FAQ list.</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>#'''Install the latest version of Phaser'''</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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 class="diffchange diffchange-inline">#:</del>We work hard so you don't have to!</div></td><td colspan="2"> </td></tr>
</table>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=158&oldid=prevWikiSysop: Protected "Top Ten Tips" ([edit=sysop] (indefinite) [move=sysop] (indefinite)) [cascading]2009-07-09T09:16:55Z<p>Protected "<a href="/index.php/Top_Ten_Tips" title="Top Ten Tips">Top Ten Tips</a>" ([edit=sysop] (indefinite) [move=sysop] (indefinite)) [cascading]</p>
<table class="diff diff-contentalign-left" data-mw="interface">
<tr class="diff-title" lang="en">
<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">Revision as of 09:16, 9 July 2009</td>
</tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div>
</td></tr></table>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Top_Ten_Tips&diff=17&oldid=prevWikiSysop: Initialization from almanac2009-06-30T12:19:49Z<p>Initialization from almanac</p>
<p><b>New page</b></p><div>#'''Use the automated search'''<br />
#:Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.<br />
#'''Search for components concurrently'''<br />
#:You should search for all components of the asymetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.<br />
#'''Search order is important'''<br />
#:The order in which you search for multiple solutions can affect your success in finding a solution. Components that account for the highest proportion of the scattering (highest completeness, highest sequence identity, and lowest B-factors) should be searched for first. If you are not sure which order is best, you can use the PERMUTATIONS ON keyword, which will search with all permutations of your input search components, but if you have a large number of different components be aware that this search will take a long time, especially if the signal from one of the components is not clear.<br />
#'''You may need to change the packing criteria'''<br />
#:Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In versions 1.x the default packing criterion is very strict - *no* clashes between C-alpha atoms are allowed. In versions 2.x the default packing criterion is relaxed so that the solutions with the lowest number of clashes are allowed, provided that number is 10 or less.<br />
#'''You may need to change the peak selection criteria'''<br />
#:By default, Phaser selects peaks that are between 75% and 100% of the difference between the top peak and the mean of the search for inclusion in the next round of the search (rotation or translation function). If you have many components in the asymmetric unit, the signal from the first rotation search may be very low, and you may need to decrease the cut-off for the rotation search to 70% or 65% using FINAL ROT SELECT PERCENT 65.<br />
#'''Beware the automated space group determination'''<br />
#:The space group is determined from the signal in the translation function search for the *first* model. If you have many components in the asymmetric unit, the signal from this search may be poor, and you should perform and exhaustive search in all the alternative space groups.<br />
#'''Homology models do not have 100% identity'''<br />
#:If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this has *not* been improved by the mutation (in fact, it has probably been made worse!). The identity you enter should thus be the same as (or less!) than that of the original sequence of your model.<br />
#'''Reduce the resolution if you can't find second and subsequent components'''<br />
#:The current algorithms have a limitation in that they do not handle the case where components of the asymmetric unit have greatly varying B-factors. This problem can be worked around by cutting the resolution to about 4 Angstroms, where the B-factor difference is less significant.<br />
#'''Look at the FAQ list'''<br />
#:If Phaser produces a strange error, or you don't understand some of the output, chances are that you are not the first person to want know what it all means. If we get asked a question three times it usually goes on the FAQ list.<br />
#'''Install the latest version of Phaser'''<br />
#:We work hard so you don't have to!</div>WikiSysop