Db2multipdb.py - Revision history

Therese: 16 revisions

2012-10-08T20:11:52Z

16 revisions

← Older revision	Revision as of 20:11, 8 October 2012
(No difference)

2012-02-08T16:56:48Z

← Older revision		Revision as of 16:56, 8 February 2012
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	The script is located at		The script is located at
	$DOCK_BASE/scripts/db2multipdb.py		$DOCK_BASE/scripts/db2multipdb.py
	or alternatively		or alternatively
	~rgc/Source/bks_src/db2multipdb.py		~rgc/Source/bks_src/db2multipdb.py

2012-02-08T16:56:39Z

← Older revision		Revision as of 16:56, 8 February 2012
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	The script is located at		The script is located at
			$DOCK_BASE/scripts/db2multipdb.py
			or alternatively
	~rgc/Source/bks_src/db2multipdb.py		~rgc/Source/bks_src/db2multipdb.py
	If you don't have python2.6 in your path you'll have to put it there or run the program like this		If you don't have python2.6 in your path you'll have to put it there or run the program like this

2010-03-05T18:50:08Z

i guess this is a tutorial now

← Older revision		Revision as of 18:50, 5 March 2010
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	Questions? contact [[User:Rgc\|Ryan Coleman]]		Questions? contact [[User:Rgc\|Ryan Coleman]]
	[[Category:Software]]		[[Category:Software]][[Category:Tutorials]]

2009-12-10T23:14:05Z

explaining error precedence

← Older revision		Revision as of 23:14, 10 December 2009
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	c is heavy atoms closer than 1.07 angstroms		c is heavy atoms closer than 1.07 angstroms
	d is no other atoms within 2.2 angstroms		d is no other atoms within 2.2 angstroms

			Note that for a given conformation, only one error of any type is reported. Type d (critical) errors take precedence over type a,b,c errors, if there is a type d error it will be reported. The number of errors of each type plus the number of models without errors always equals the total number of models.

	Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.		Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.

2009-12-10T23:10:57Z

← Older revision		Revision as of 23:10, 10 December 2009
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	Questions? contact [[User:Rgc\|Ryan Coleman]]		Questions? contact [[User:Rgc\|Ryan Coleman]]
			[[Category:Software]]

2009-12-10T23:05:51Z

changing formatting

← Older revision		Revision as of 23:05, 10 December 2009
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	P00000008 being processed now 1		P00000008 being processed now 1
	P00000008 1 errors of each type: 542 0 0 0 no errors: 817 total models 1359		P00000008 1 errors of each type: 542 0 0 0 no errors: 817 total models 1359
			roughly interpreted as:
	zincid^^^ #times zincid seen^^^^ a^^ b c d ^^^^^^^^^^ #without errors #total		zincid^^^ #times zincid seen^^^^ a^^ b c d ^^^^^^^^^^ #without errors #total

2009-12-10T23:05:01Z

talking about pdb file output

← Older revision		Revision as of 23:05, 10 December 2009
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	Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.		Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.

			If pdb output is not suppressed files will be written named P00000008.001.pdb where the first 9 characters are the ZINCID read from the db file, then a unique counter (since a .db file can contain multiple .db entries for one ZINCID). Each pdb file is a normal pdb file, with each MODEL as one unique conformation produced. Obviously these can be quite large and writing them to disk takes much longer than anything else the code does. If you load this pdb file in PyMOL for instance and then hit the 'play' button it will go through the entire set. Obviously other post-processing or conversion is possible.

	Questions? contact [[User:Rgc\|Ryan Coleman]]		Questions? contact [[User:Rgc\|Ryan Coleman]]

2009-12-10T23:01:06Z

← Older revision		Revision as of 23:01, 10 December 2009
Line 31:		Line 31:
	Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.		Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.

	Questions? contact [[Rgc\|Ryan Coleman]]		Questions? contact [[User:Rgc\|Ryan Coleman]]

2009-12-10T23:00:45Z

← Older revision		Revision as of 23:00, 10 December 2009
Line 31:		Line 31:
	Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.		Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should <i>not</i> occur but have been known to previously.

	Questions? contact [[Ryan Coleman~~\|Rgc~~]]		Questions? contact [[Rgc\|Ryan Coleman]]