PdbStat - Revision history

Jma at 14:24, 5 October 2011

2011-10-05T14:24:34Z

← Older revision		Revision as of 14:24, 5 October 2011
Line 209:		Line 209:
	write rdc cns [filename_rdc2.tbl] 2		write rdc cns [filename_rdc2.tbl] 2
	</pre>		</pre>
	~~==== ====~~

	2.  Reading and converting hydrogen bond constraints.<br>		2.  Reading and converting hydrogen bond constraints.<br>
Line 231:		Line 230:
	write cons cns [filename_metal.tbl] #write metal ion constraints in CNS format		write cons cns [filename_metal.tbl] #write metal ion constraints in CNS format
	</pre>		</pre>
	~~==== ====~~		4.  Converting constraints to Rosetta format<br>

			Example:<br>
			<pre># If you have already loaded cons and aco constraints into PdbStat:

			write noe rosetta [outputfile]
			write aco rosetta [outputfile]
			</pre>


	~~====     ====~~

	== '''References''' ==		== '''References''' ==

	[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>		[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>

Jma at 14:20, 5 October 2011

2011-10-05T14:20:46Z

← Older revision		Revision as of 14:20, 5 October 2011
Line 217:		Line 217:

	rea coo pdb final.pdb #read CYANA pdb file		rea coo pdb final.pdb #read CYANA pdb file
	rea upl cyana hbonds.upl #read CYANA hbonds.upl file		rea upl cyana hbonds.upl #read CYANA hbonds upl file
	rea lol cyana hbonds.lol #read CYANA hbonds.lol		rea lol cyana hbonds.lol #read CYANA hbonds lol file
	write cons cns [filename_hbond.tbl] #write hbond constraints in CNS format		write cons cns [filename_hbond.tbl] #write hbond constraints in CNS format
	</pre>		</pre>
			3.  Reading and converting metal ion constraints.<br>

			Example:<br>
			<pre># reading metal ion constraints in CYANA format and converting to CNS:

			rea coo pdb final.pdb #read CYANA pdb file
			rea upl cyana metal.upl #read CYANA metal ion upl file
			rea lol cyana metal.lol #read CYANA metal ion lol
			write cons cns [filename_metal.tbl] #write metal ion constraints in CNS format
			</pre>
			==== ====

	====     ====		====     ====

Jma at 14:18, 5 October 2011

2011-10-05T14:18:11Z

← Older revision		Revision as of 14:18, 5 October 2011
Line 208:		Line 208:
	write rdc cns [filename_rdc1.tbl] 1		write rdc cns [filename_rdc1.tbl] 1
	write rdc cns [filename_rdc2.tbl] 2		write rdc cns [filename_rdc2.tbl] 2


	</pre>		</pre>
	==== ====		==== ====
Line 222:		Line 220:
	rea lol cyana hbonds.lol #read CYANA hbonds.lol		rea lol cyana hbonds.lol #read CYANA hbonds.lol
	write cons cns [filename_hbond.tbl] #write hbond constraints in CNS format		write cons cns [filename_hbond.tbl] #write hbond constraints in CNS format


	</pre>		</pre>
	~~==== ====~~

	====     ====		====     ====

Jma at 14:16, 5 October 2011

2011-10-05T14:16:23Z

← Older revision		Revision as of 14:16, 5 October 2011
Line 194:		Line 194:
	Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.  Below is a summary of new functions added to the program.<br>		Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.  Below is a summary of new functions added to the program.<br>

	1.  Reading and ~~anlyzing~~ residual dipolar couplings.<br>		1.  Reading and analyzing residual dipolar couplings.<br>

	~~Example:<br>~~


			Example:<br>
	<pre># reading two rdc files in cyana format (i.e., after a CYANA 3.0 structure calculation with RDCs):		<pre># reading two rdc files in cyana format (i.e., after a CYANA 3.0 structure calculation with RDCs):

Line 213:		Line 211:

	</pre>		</pre>
	==== ~~<br>~~ ====		==== ====

			2.  Reading and converting hydrogen bond constraints.<br>

			Example:<br>
			<pre># reading hydrogen bond constraints in CYANA format and converting to CNS:

			rea coo pdb final.pdb #read CYANA pdb file
			rea upl cyana hbonds.upl #read CYANA hbonds.upl file
			rea lol cyana hbonds.lol #read CYANA hbonds.lol
			write cons cns [filename_hbond.tbl] #write hbond constraints in CNS format


			</pre>
			==== ====

	~~<br>~~		====     ====

	== '''References''' ==		== '''References''' ==

	[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>		[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>

Jma at 14:11, 5 October 2011

2011-10-05T14:11:18Z

@@ Line 192: / Line 192: @@
 ==== Version 5.4<br>  ====
-Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.&nbsp; <br>
+Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.&nbsp; Below is a summary of new functions added to the program.<br>
 == '''References'''  ==
 [http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>

Jma at 13:56, 5 October 2011

2011-10-05T13:56:09Z

← Older revision		Revision as of 13:56, 5 October 2011
Line 187:		Line 187:

	<br>		<br>
	~~<span style="font-weight: bold;">Updates</span><br> ==~~

	===~~= Version 5.4~~<br> ====		== <span style="font-weight: bold;">Updates</span> ==

	Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.  <br>		==== Version 5.4<br> ====

			Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.  <br>

	== '''References''' ==		== '''References''' ==

	[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>		[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>

Jma at 13:54, 5 October 2011

2011-10-05T13:54:44Z

← Older revision		Revision as of 13:54, 5 October 2011
Line 187:		Line 187:

	<br>		<br>
			<span style="font-weight: bold;">Updates</span><br> ==

			==== Version 5.4<br> ====

			Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.  <br>

	== '''References''' ==		== '''References''' ==

	[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>		[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>

Jma at 17:01, 5 January 2010

2010-01-05T17:01:47Z

← Older revision		Revision as of 17:01, 5 January 2010
Line 190:		Line 190:
	== '''References''' ==		== '''References''' ==

	[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>		[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795. ]<br>[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. ''J. Am. Chem. Soc. 127'', 1665-1674. ]<br>[http://www3.interscience.wiley.com/journal/110445756/abstract 3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. ''Proteins 59'', 673-686. ]<br>

	~~-- JimAramini - 14 Aug 2008~~

Jma at 20:48, 25 December 2009

2009-12-25T20:48:53Z

← Older revision		Revision as of 20:48, 25 December 2009
Line 85:		Line 85:
	write coo pdb [overlayed file] #write overlayed coordinates</onlyinclude>		write coo pdb [overlayed file] #write overlayed coordinates</onlyinclude>

	Next, open the overlayed coordinates in Molmol and get the desired rotation. Use <tt>writetransform</tt> command to write the rotation matrix to a file. <br> Back in PdbStat: <br> <onlyinclude>rea coo pdb [overlayed.pdb] #read the overlayed coordinates (all models)		Next, open the overlayed coordinates in Molmol and get the desired rotation. Use <tt>writetransform</tt> command to write the rotation matrix to a file. <br> Back in PdbStat: <br> <onlyinclude>
			rea coo pdb [overlayed.pdb] #read the overlayed coordinates (all models)
	rotate file [filename] #apply rotation matrix		rotate file [filename] #apply rotation matrix
	write coo pdb [final.pdb] #write new coordinates		write coo pdb [final.pdb] #write new coordinates
	to iupac #converts atom nomenclature to IUPAC		to iupac #converts atom nomenclature to IUPAC
	write coo pdb [final_iupac.pdb] #write IUPAC coordinates for RPF analysis</onlyinclude>		write coo pdb [final_iupac.pdb] #write IUPAC coordinates for RPF analysis</onlyinclude>

	==== Selecting specific models / residues / atoms. ====		==== Selecting specific models / residues / atoms. ====
Line 185:		Line 186:
	> MAIN_cntct: atom type (hydr, heavy, all) ?:_ hydr #writes a postscript file</onlyinclude>		> MAIN_cntct: atom type (hydr, heavy, all) ?:_ hydr #writes a postscript file</onlyinclude>

	<br>		<br>

	== '''References''' ==		== '''References''' ==

Jma at 20:40, 25 December 2009

2009-12-25T20:40:18Z

← Older revision		Revision as of 20:40, 25 December 2009
Line 72:		Line 72:
	==== Preparation of final CNS coordinates for PDB deposition ====		==== Preparation of final CNS coordinates for PDB deposition ====

	Before we deposit our final coordinates we would like to order our models in order of lowest conformation energy. Also, we want to perform backbone superposition of the coordinates using ordered [S(phi) + S(psi) > 1.8] residues only. Finally, we want to rotate the ensemble to a desired orientation, which will be the orientation that appears when a user downloads ~~out~~ coordinates from the Protein Data Bank (www.rcsb.org). The final coordinates are saved in the original (CNS) format and IUPAC format for RPF analysis [2].		Before we deposit our final coordinates we would like to order our models in order of lowest conformation energy. Also, we want to perform backbone superposition of the coordinates using ordered [S(phi) + S(psi) > 1.8] residues only. Finally, we want to rotate the ensemble to a desired orientation, which will be the orientation that appears when a user downloads our coordinates from the Protein Data Bank (www.rcsb.org). The final coordinates are saved in the original (CNS) format and IUPAC format for RPF analysis [2].

	To prepare the final coordinates file for PDB deposition use the following protocol:		To prepare the final coordinates file for PDB deposition use the following protocol:
Line 89:		Line 89:
	write coo pdb [final.pdb] #write new coordinates		write coo pdb [final.pdb] #write new coordinates
	to iupac #converts atom nomenclature to IUPAC		to iupac #converts atom nomenclature to IUPAC
	write coo pdb [final_iupac.pdb] #write IUPAC coordinates for RPF analysis</onlyinclude>		write coo pdb [final_iupac.pdb] #write IUPAC coordinates for RPF analysis</onlyinclude>

	==== Selecting specific models / residues / atoms. ====		==== Selecting specific models / residues / atoms. ====