http://wiki.docking.org/index.php?title=DUMM1&feed=atom&action=historyDUMM1 - Revision history2024-03-28T22:08:13ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=DUMM1&diff=1203&oldid=prevTherese: 32 revisions2012-10-08T20:11:50Z<p>32 revisions</p>
<p><b>New page</b></p><div>== Attendees & Time==<br />
<br />
Sarah, Alessandro, Francesco, Hao, Michael, Pascal, Peter<br />
<br />
Date: June 04, 2008<br />
<br />
'''Next DUM on Wednesday, July 2, 2008'''<br />
<br />
== Hardware updates==<br />
<br />
''Pascal:'' 8&times;44 "[http://insider.ucsf.edu/2007/july/spotlight_4.html Fight for Mike]" machines will arrive shortly. Problem: how to coordinate the high number of machines to write to disk w/o affecting the other users &rArr; what gets written to disk during a [[DOCK]] run?<br />
<br><br />
''Michael:'' three big files: test.eel1, test.1 and OUTDOCK. test.1 should be optional. test.eel1 and OUTDOCK are gzipped in the most recent version of DOCK (part of [[dock67]]). Problem: [[DOCK]] writes test.* at the end of the run &rArr; maybe streamline the process?<br />
<br><br />
''Pascal:'' solution is probably to write to scratch and then cp files over at the end.<br />
<br />
''John:'' Michael's gzipped output helps. Also set restart_interval to big value (100000) to prevent heavy disk writes. As of now, the new machines seem to have been absorbed with no performance problems.<br />
<br />
==Software updates==<br />
<br />
===dock67 | solvmap===<br />
<br />
''Michael:'' [[dock67]] has been released. It contains a new version of <tt>[[solvmap]]</tt>, which has a bugfix for the "blank lines bug" that caused the solvation penalties to be wrong. The output of the new version can be recognized by the fact that the last three numbers on the first line are floats. <br />
<br />
===runAMSOL3.csh===<br />
<br />
''Michael:'' use <tt>runAMSOL3.csh WAIT</tt> to use [http://comp.chem.umn.edu/amsol AMSOL] when preparing database files, so you get the correct cavitation term.<br />
<br />
===file2file.py===<br />
<br />
''Michael:'' <tt>file2file.py</tt> has been improved: uses [http://www.tripos.com/mol2/atom_types.html SYBYL atom types]; charged molecules are handled correctly.<br />
<br />
===dbgen.csh===<br />
<br />
''Michael:'' more tools for database generation are available: <tt>dbgen.csh</tt> uses the most recent version of the procedure without using [http://zinc.docking.org ZINC], ensuring the molecules are all generated from scratch. Commandline: <tt>dbgen.csh my.smi [optional protonation type]</tt><br />
<br />
===decoys.py===<br />
<br />
''Michael:'' <tt>decoys.py</tt> builds [[DUD]]-style set of decoys. Help accessible with <tt>decoys.py -h</tt>. Executable can be found at <tt>~mysinger/code/dud/trunk/decoys.py</tt>. <br />
<br />
===database generation===<br />
<br />
''Michael:'' if one has to generate large amounts of database files, you can put the jobs on the cluster. Use <tt>dbstart.csh ./dbname.smi</tt> on sgehead to start the jobs and <tt>dbend.csh</tt> to collect them when they are done. If <tt>dbname.smi</tt> contains more than 1000 molecules, break it down to smaller subparts.<br />
<br />
==[[DOCK]] updates ==<br />
<br />
===dock67===<br />
<br />
''Michael:'' the most recent version of [[DOCK]] (part of [[dock67]]) gzips test.eel1 and OUTDOCK.<br />
<br />
===Requests/Improvements===<br />
<br />
''Hao:'' it might be good to include an option in [[DOCK]] to be able to write out more than one pose per molecule.<br><br />
''Michael:'' this is part of my orals proposal.<br />
<br />
== Varia ==<br />
<br />
===ZINC history===<br />
<br />
''Sarah:'' how to keep old [http://zinc.docking.org ZINC] versions and ensure that molecules are the same, especially in order to be able to reproduce calculations?<br />
<br><br />
''John answers:'' ZINC 5, 6, 7 are all still on line and available. <br />
<br><br />
''Pascal:'' is there a way to find out which tools were used to build a certain molecule?<br />
<br><br />
''Peter:'' how to rebuild molecules?<br />
<br><br />
''Francesco:'' there is a script called <tt>rebuildit.pl</tt> which will schedule the molecules in question for rebuilding in [http://zinc.docking.org ZINC]. Commandline: <tt>rebuildit.pl < list_of_zinc_ids</tt>.<br><br />
''Michael:'' the molecule files are located on <tt>/raid2/db/XX/YY/PROTXXYY.*</tt>. Note this is the protomer id and not the zinc id.<br />
<br />
===Knowledge managment===<br />
<br />
''Peter:'' how do we make software changes visible to the internal users?<br><br />
''Michael/Peter/Sarah:'' keep minutes and put them up on the wiki. Ideally include subpages and changelogs for the software items. Make sure that everyone has access to the latest versions of software/scripts/testcases for evaluation purposes.<br><br />
''Pascal/Michael:'' make more consistent use of the CVS to omit consecutive numbering of scripts.<br />
<br />
<br />
[[Category:DUMM]]<br />
<br />
&rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]</div>Theresehttp://wiki.docking.org/index.php?title=DUMM1&diff=1200&oldid=prevFrodo: /* Knowledge managment */2008-07-10T03:56:24Z<p><span dir="auto"><span class="autocomment">Knowledge managment</span></span></p>
<p><b>New page</b></p><div>== Attendees & Time==<br />
<br />
Sarah, Alessandro, Francesco, Hao, Michael, Pascal, Peter<br />
<br />
Date: June 04, 2008<br />
<br />
'''Next DUM on Wednesday, July 2, 2008'''<br />
<br />
== Hardware updates==<br />
<br />
''Pascal:'' 8&times;44 "[http://insider.ucsf.edu/2007/july/spotlight_4.html Fight for Mike]" machines will arrive shortly. Problem: how to coordinate the high number of machines to write to disk w/o affecting the other users &rArr; what gets written to disk during a [[DOCK]] run?<br />
<br><br />
''Michael:'' three big files: test.eel1, test.1 and OUTDOCK. test.1 should be optional. test.eel1 and OUTDOCK are gzipped in the most recent version of DOCK (part of [[dock67]]). Problem: [[DOCK]] writes test.* at the end of the run &rArr; maybe streamline the process?<br />
<br><br />
''Pascal:'' solution is probably to write to scratch and then cp files over at the end.<br />
<br />
''John:'' Michael's gzipped output helps. Also set restart_interval to big value (100000) to prevent heavy disk writes. As of now, the new machines seem to have been absorbed with no performance problems.<br />
<br />
==Software updates==<br />
<br />
===dock67 | solvmap===<br />
<br />
''Michael:'' [[dock67]] has been released. It contains a new version of <tt>[[solvmap]]</tt>, which has a bugfix for the "blank lines bug" that caused the solvation penalties to be wrong. The output of the new version can be recognized by the fact that the last three numbers on the first line are floats. <br />
<br />
===runAMSOL3.csh===<br />
<br />
''Michael:'' use <tt>runAMSOL3.csh WAIT</tt> to use [http://comp.chem.umn.edu/amsol AMSOL] when preparing database files, so you get the correct cavitation term.<br />
<br />
===file2file.py===<br />
<br />
''Michael:'' <tt>file2file.py</tt> has been improved: uses [http://www.tripos.com/mol2/atom_types.html SYBYL atom types]; charged molecules are handled correctly.<br />
<br />
===dbgen.csh===<br />
<br />
''Michael:'' more tools for database generation are available: <tt>dbgen.csh</tt> uses the most recent version of the procedure without using [http://zinc.docking.org ZINC], ensuring the molecules are all generated from scratch. Commandline: <tt>dbgen.csh my.smi [optional protonation type]</tt><br />
<br />
===decoys.py===<br />
<br />
''Michael:'' <tt>decoys.py</tt> builds [[DUD]]-style set of decoys. Help accessible with <tt>decoys.py -h</tt>. Executable can be found at <tt>~mysinger/code/dud/trunk/decoys.py</tt>. <br />
<br />
===database generation===<br />
<br />
''Michael:'' if one has to generate large amounts of database files, you can put the jobs on the cluster. Use the script <tt>dbstart.csh</tt> on sgehead to start the jobs and <tt>dbend.csh</tt> to collect them when they are done.<br />
<br />
==[[DOCK]] updates ==<br />
<br />
===dock67===<br />
<br />
''Michael:'' the most recent version of [[DOCK]] (part of [[dock67]]) gzips test.eel1 and OUTDOCK.<br />
<br />
===Requests/Improvements===<br />
<br />
''Hao:'' it might be good to include an option in [[DOCK]] to be able to write out more than one pose per molecule.<br><br />
''Michael:'' this is part of my orals proposal.<br />
<br />
== Varia ==<br />
<br />
===ZINC history===<br />
<br />
''Sarah:'' how to keep old [http://zinc.docking.org ZINC] versions and ensure that molecules are the same, especially in order to be able to reproduce calculations?<br />
<br><br />
''John answers:'' ZINC 5, 6, 7 are all still on line and available. <br />
<br><br />
''Pascal:'' is there a way to find out which tools were used to build a certain molecule?<br />
<br><br />
''Peter:'' how to rebuild molecules?<br />
<br><br />
''Francesco:'' there is a script called <tt>rebuildit.pl</tt> which will schedule the molecules in question for rebuilding in [http://zinc.docking.org ZINC]. Commandline: <tt>rebuildit.pl < list_of_zinc_ids</tt>.<br><br />
''Michael:'' the molecule files are located on <tt>/raid2/db/XX/YY/PROTXXYY.*</tt>. Note this is the protomer id and not the zinc id.<br />
<br />
===Knowledge managment===<br />
<br />
''Peter:'' how do we make software changes visible to the internal users?<br><br />
''Michael/Peter/Sarah:'' keep minutes and put them up on the wiki. Ideally include subpages and changelogs for the software items. Make sure that everyone has access to the latest versions of software/scripts/testcases for evaluation purposes.<br><br />
''Pascal/Michael:'' make more consistent use of the CVS to omit consecutive numbering of scripts.<br />
<br />
<br />
[[Category:DUMM]]<br />
<br />
back to [[Dock_Users%27_Meeting_Minutes_%28DUMM%29]]</div>Frodohttp://wiki.docking.org/index.php?title=DUMM1&diff=1194&oldid=prevFrodo: /* ZINC history */2008-07-09T18:44:53Z<p><span dir="auto"><span class="autocomment">ZINC history</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<col class="diff-content" />
<col class="diff-marker" />
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<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 18:44, 9 July 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l57">Line 57:</td>
<td colspan="2" class="diff-lineno">Line 57:</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>''Sarah:'' how to keep old [http://zinc.docking.org ZINC] versions and ensure that molecules are the same, especially in order to be able to reproduce calculations?</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>''Sarah:'' how to keep old [http://zinc.docking.org ZINC] versions and ensure that molecules are the same, especially in order to be able to reproduce calculations?</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;">''John answers:'' ZINC 5, 6, 7 are all still on line and available. </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></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><br></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>''Pascal:'' is there a way to find out which tools were used to build a certain molecule?</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>''Pascal:'' is there a way to find out which tools were used to build a certain molecule?</div></td></tr>
<!-- diff cache key wikidb:diff::1.12:old-1193:rev-1194 -->
</table>Frodohttp://wiki.docking.org/index.php?title=DUMM1&diff=1193&oldid=prevFrodo: /* Hardware updates */2008-07-09T18:42:32Z<p><span dir="auto"><span class="autocomment">Hardware updates</span></span></p>
<p><b>New page</b></p><div>== Attendees ==<br />
<br />
Sarah, Alessandro, Francesco, Hao, Michael, Pascal, Peter<br />
<br />
'''Next DUM on Wednesday, July 2, 2008'''<br />
<br />
== Hardware updates==<br />
<br />
''Pascal:'' 8&times;44 "[http://insider.ucsf.edu/2007/july/spotlight_4.html Fight for Mike]" machines will arrive shortly. Problem: how to coordinate the high number of machines to write to disk w/o affecting the other users &rArr; what gets written to disk during a [[DOCK]] run?<br />
<br><br />
''Michael:'' three big files: test.eel1, test.1 and OUTDOCK. test.1 should be optional. test.eel1 and OUTDOCK are gzipped in the most recent version of DOCK (part of [[dock67]]). Problem: [[DOCK]] writes test.* at the end of the run &rArr; maybe streamline the process?<br />
<br><br />
''Pascal:'' solution is probably to write to scratch and then cp files over at the end.<br />
<br />
''John:'' Michael's gzipped output helps. Also set restart_interval to big value (100000) to prevent heavy disk writes. As of now, the new machines seem to have been absorbed with no performance problems.<br />
<br />
==Software updates==<br />
<br />
===dock67 | solvmap===<br />
<br />
''Michael:'' [[dock67]] has been released. It contains a new version of <tt>[[solvmap]]</tt>, which has a bugfix for the "blank lines bug" that caused the solvation penalties to be wrong. The output of the new version can be recognized by the fact that the last three numbers on the first line are floats. <br />
<br />
===runAMSOL3.csh===<br />
<br />
''Michael:'' use <tt>runAMSOL3.csh WAIT</tt> to use [http://comp.chem.umn.edu/amsol AMSOL] when preparing database files, so you get the correct cavitation term.<br />
<br />
===file2file.py===<br />
<br />
''Michael:'' <tt>file2file.py</tt> has been improved: uses [http://www.tripos.com/mol2/atom_types.html SYBYL atom types]; charged molecules are handled correctly.<br />
<br />
===dbgen.csh===<br />
<br />
''Michael:'' more tools for database generation are available: <tt>dbgen.csh</tt> uses the most recent version of the procedure without using [http://zinc.docking.org ZINC], ensuring the molecules are all generated from scratch. Commandline: <tt>dbgen.csh my.smi [optional protonation type]</tt><br />
<br />
===decoys.py===<br />
<br />
''Michael:'' <tt>decoys.py</tt> builds [[DUD]]-style set of decoys. Help accessible with <tt>decoys.py -h</tt>. Executable can be found at <tt>~mysinger/code/dud/trunk/decoys.py</tt>. <br />
<br />
===database generation===<br />
<br />
''Michael:'' if one has to generate large amounts of database files, you can put the jobs on the cluster. Use the script <tt>dbstart.csh</tt> on sgehead to start the jobs and <tt>dbend.csh</tt> to collect them when they are done.<br />
<br />
==[[DOCK]] updates ==<br />
<br />
===dock67===<br />
<br />
''Michael:'' the most recent version of [[DOCK]] (part of [[dock67]]) gzips test.eel1 and OUTDOCK.<br />
<br />
===Requests/Improvements===<br />
<br />
''Hao:'' it might be good to include an option in [[DOCK]] to be able to write out more than one pose per molecule.<br><br />
''Michael:'' this is part of my orals proposal.<br />
<br />
== Varia ==<br />
<br />
===ZINC history===<br />
<br />
''Sarah:'' how to keep old [http://zinc.docking.org ZINC] versions and ensure that molecules are the same, especially in order to be able to reproduce calculations?<br />
<br><br />
''Pascal:'' is there a way to find out which tools were used to build a certain molecule?<br />
<br><br />
''Peter:'' how to rebuild molecules?<br />
<br><br />
''Francesco:'' there is a script called <tt>rebuildit.pl</tt> which will schedule the molecules in question for rebuilding in [http://zinc.docking.org ZINC]. Commandline: <tt>rebuildit.pl < list_of_zinc_ids</tt>.<br><br />
''Michael:'' the molecule files are located on <tt>/raid2/db/XX/YY/PROTXXYY.*</tt>. Note this is the protomer id and not the zinc id.<br />
<br />
===Knowledge managment===<br />
<br />
''Peter:'' how do we make software changes visible to the internal users?<br><br />
''Michael/Peter/Sarah:'' keep minutes and put them up on the wiki. Ideally include subpages and changelogs for the software items. Make sure that everyone has access to the latest versions of software/scripts/testcases for evaluation purposes.<br><br />
''Pascal/Michael:'' make more consistent use of the CVS to omit consecutive numbering of scripts.<br />
<br />
--[http://shoichetlab.compbio.ucsf.edu/~kolb Kolb] 16:08, 9 June 2008 (PDT)</div>Frodohttp://wiki.docking.org/index.php?title=DUMM1&diff=1186&oldid=prevMysinger: /* Varia */2008-06-10T05:35:59Z<p><span dir="auto"><span class="autocomment">Varia</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<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 05:35, 10 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l59">Line 59:</td>
<td colspan="2" class="diff-lineno">Line 59:</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><br></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><br></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>''Francesco:'' there is a script called <tt>rebuildit.pl</tt> which will schedule the molecules in question for rebuilding in [http://zinc.docking.org ZINC]. Commandline: <tt>rebuildit.pl list_of_zinc_ids</tt>.<br></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>''Francesco:'' there is a script called <tt>rebuildit.pl</tt> which will schedule the molecules in question for rebuilding in [http://zinc.docking.org ZINC]. Commandline: <tt>rebuildit.pl list_of_zinc_ids</tt>.<br></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>''Michael:'' the molecule files are located on <tt>/raid2</tt>.</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>''Michael:'' the molecule files are located on <tt>/raid2<ins style="font-weight: bold; text-decoration: none;">/db/XX/YY/PROTXXYY.*</ins></tt><ins style="font-weight: bold; text-decoration: none;">. Note this is the protomer id and not the zinc id</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>'''Knowledge managment'''</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>'''Knowledge managment'''</div></td></tr>
</table>Mysingerhttp://wiki.docking.org/index.php?title=DUMM1&diff=1185&oldid=prevMysinger: /* Hardware updates */2008-06-10T05:33:34Z<p><span dir="auto"><span class="autocomment">Hardware updates</span></span></p>
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<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 05:33, 10 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7">Line 7:</td>
<td colspan="2" class="diff-lineno">Line 7:</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>''Pascal:'' 8x44 "[http://insider.ucsf.edu/2007/july/spotlight_4.html Fight for Mike]" machines will arrive shortly. Problem: how to coordinate the high number of machines to write to disk w/o affecting the other users &rArr; what gets written to disk during a [[DOCK]] 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>''Pascal:'' 8x44 "[http://insider.ucsf.edu/2007/july/spotlight_4.html Fight for Mike]" machines will arrive shortly. Problem: how to coordinate the high number of machines to write to disk w/o affecting the other users &rArr; what gets written to disk during a [[DOCK]] run?</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><br></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><br></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>''Michael:'' three big files: test.eel1, test.1 and OUTDOCK. test.1 should be optional. test.eel1 and OUTDOCK are gzipped in the most recent version of DOCK (part of [[dock67]]). Problem: [[DOCK]] <del style="font-weight: bold; text-decoration: none;">rewrites OUTDOCK </del>at the end of the run &rArr; maybe streamline the process?</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>''Michael:'' three big files: test.eel1, test.1 and OUTDOCK. test.1 should be optional. test.eel1 and OUTDOCK are gzipped in the most recent version of DOCK (part of [[dock67]]). Problem: [[DOCK]] <ins style="font-weight: bold; text-decoration: none;">writes test.* </ins>at the end of the run &rArr; maybe streamline the process?</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><br></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><br></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>''Pascal:'' solution is probably to write to scratch and then cp files over at the end.</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>''Pascal:'' solution is probably to write to scratch and then cp files over at the end.</div></td></tr>
</table>Mysingerhttp://wiki.docking.org/index.php?title=DUMM1&diff=1184&oldid=prevMysinger: /* Software updates */2008-06-10T05:32:24Z<p><span dir="auto"><span class="autocomment">Software updates</span></span></p>
<p><b>New page</b></p><div>== Attendees ==<br />
<br />
Sarah, Alessandro, Francesco, Hao, Michael, Pascal, Peter<br />
<br />
== Hardware updates==<br />
<br />
''Pascal:'' 8x44 "[http://insider.ucsf.edu/2007/july/spotlight_4.html Fight for Mike]" machines will arrive shortly. Problem: how to coordinate the high number of machines to write to disk w/o affecting the other users &rArr; what gets written to disk during a [[DOCK]] run?<br />
<br><br />
''Michael:'' three big files: test.eel1, test.1 and OUTDOCK. test.1 should be optional. test.eel1 and OUTDOCK are gzipped in the most recent version of DOCK (part of [[dock67]]). Problem: [[DOCK]] rewrites OUTDOCK at the end of the run &rArr; maybe streamline the process?<br />
<br><br />
''Pascal:'' solution is probably to write to scratch and then cp files over at the end.<br />
<br />
==Software updates==<br />
<br />
'''dock67''' | '''solvmap'''<br />
<br />
''Michael:'' [[dock67]] has been released. It contains a new version of <tt>[[solvmap]]</tt>, which has a bugfix for the "blank lines bug" that caused the solvation penalties to be wrong. The output of the new version can be recognized by the fact that the last three numbers on the first line are floats. <br />
<br />
'''runAMSOL3.csh'''<br />
<br />
''Michael:'' use <tt>runAMSOL3.csh WAIT</tt> to use [http://comp.chem.umn.edu/amsol AMSOL] when preparing database files, so you get the correct cavitation term.<br />
<br />
'''file2file.py'''<br />
<br />
''Michael:'' <tt>file2file.py</tt> has been improved: uses [http://www.tripos.com/mol2/atom_types.html SYBYL atom types]; charged molecules are handled correctly.<br />
<br />
'''dbgen.csh'''<br />
<br />
''Michael:'' more tools for database generation are available: <tt>dbgen.csh</tt> uses the most recent version of the procedure without using [http://zinc.docking.org ZINC], ensuring they are all generated from scratch. Commandline: <tt>dbgen.csh my.smi [optional protonation type]</tt><br />
<br />
'''decoys.py'''<br />
<br />
''Michael:'' <tt>decoys.py</tt> builds [[DUD]]-style set of decoys. Help accessible with <tt>decoys.py -h</tt>. Executable can be found at <tt>~mysinger/code/dud/trunk/decoys.py</tt>. <br />
<br />
'''database generation'''<br />
<br />
''Michael:'' if one has to generate large amounts of database files, you can put the jobs on the cluster. Use the script <tt>dbstart.csh</tt> on sgehead to start the jobs and <tt>dbend.csh</tt> to collect them when they are done.<br />
<br />
==[[DOCK]] updates ==<br />
<br />
'''dock67'''<br />
<br />
''Michael:'' the most recent version of [[DOCK]] (part of [[dock67]]) gzips test.eel1 and OUTDOCK.<br />
<br />
'''Requests/Improvements'''<br />
<br />
''Hao:'' it might be good to include an option in [[DOCK]] to be able to write out more than one pose per molecule.<br><br />
''Michael:'' this is part of my orals proposal.<br />
<br />
== Varia ==<br />
<br />
'''ZINC history'''<br />
<br />
''Sarah:'' how to keep old [http://zinc.docking.org ZINC] versions and ensure that molecules are the same, especially in order to be able to reproduce calculations?<br />
<br><br />
''Pascal:'' is there a way to find out which tools were used to build a certain molecule?<br />
<br><br />
''Peter:'' how to rebuild molecules?<br />
<br><br />
''Francesco:'' there is a script called <tt>rebuildit.pl</tt> which will schedule the molecules in question for rebuilding in [http://zinc.docking.org ZINC]. Commandline: <tt>rebuildit.pl list_of_zinc_ids</tt>.<br><br />
''Michael:'' the molecule files are located on <tt>/raid2</tt>.<br />
<br />
'''Knowledge managment'''<br />
<br />
''Peter:'' how do we make software changes visible to the internal users?<br><br />
''Michael/Peter/Sarah:'' keep minutes and put them up on the wiki. Ideally include subpages and changelogs for the software items. Make sure that everyone has access to the latest versions of software/scripts/testcases for evaluation purposes.<br><br />
''Pascal/Michael:'' make more consistent use of the CVS to omit consecutive numbering of scripts.<br />
<br />
--[http://shoichetlab.compbio.ucsf.edu/~kolb Kolb] 16:08, 9 June 2008 (PDT)</div>Mysinger