ChargeCalculator:Interpretation of results - Revision history

Crina: /* 3D Model */

2015-05-29T17:12:15Z

3D Model

← Older revision		Revision as of 17:12, 29 May 2015
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	[[File:ACC FirstTimeUserGuide 18.jpg\|thumb\|right\|650px\| The '''3D Model tab''' displays a 3D model of your molecule, based either on atomic or residue resolution. The contents of the visualization window are dictated by the panel on the left.]]		[[File:ACC FirstTimeUserGuide 18.jpg\|thumb\|right\|650px\| The '''3D Model tab''' displays a 3D model of your molecule, based either on atomic or residue resolution. The contents of the visualization window are dictated by the panel on the left.]]

	'''ACC''' allows a few basic charge visualization options to aid in interpreting the results of the atomic charge calculation. You may need to update your browser and driver version to be able to run the 3D visualizer (see the [[ChargeCalculator:Technical_details#Requirements \| requirements]]). The panels on the left dictate contents of the visualization window on the right, which allows you to display and manipulate with a ''3D model of your molecule colored according to charges''. The legend for mouse controls for manipulating with the 3D model (rotation, zoom) is available in the right bottom corner of the visualization window.		'''ACC''' allows a few basic charge visualization options to aid in interpreting the results of the atomic charge calculation. You may need to update your browser and driver version to be able to run the 3D visualizer (see the [[ChargeCalculator:Technical_details#Requirements \| requirements]]). The panels on the left dictate the contents of the visualization window on the right, which allows you to display and manipulate with a ''3D model of your molecule colored according to charges''. The legend for mouse controls for manipulating with the 3D model (rotation, zoom) is available in the right bottom corner of the visualization window.

	Note that 3D visualization is generally memory consuming, so you should consider the settings before attempting to visualize the 3D model of your molecule. '''ACC''' allows you to customize the 3D model of the molecule in several ways. If you would like to revert to the default visualization settings suggested by '''ACC''', click ''Set default parameters''. If you feel confident that your visualization settings are suitable, click ''Update'' to display the 3D model of your molecule colored according to charges. You may need to use the ''Update'' button several times as you adjust the visualization state, as some changes will not take effect otherwise.		Note that 3D visualization is generally memory consuming, so you should consider the settings before attempting to visualize the 3D model of your molecule. '''ACC''' allows you to customize the 3D model of the molecule in several ways. If you would like to revert to the default visualization settings suggested by '''ACC''', click ''Set default parameters''. If you feel confident that your visualization settings are suitable, click ''Update'' to display the 3D model of your molecule colored according to charges. You may need to use the ''Update'' button several times as you adjust the visualization state, as some changes will not take effect otherwise.

Crina: /* Summary */

2015-05-29T16:56:17Z

Summary

← Older revision		Revision as of 16:56, 29 May 2015
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	Note that multiple ''jobs'' may have been run for this molecule. A job is defined based on the molecule and its total charge, along with the EEM parameter set and computation method used. Each job produces a distinct ''set of charges'' with a unique ID encoding the EEM parameter set, method and total molecular charge. If the original input file contained values of atomic charges, these are also stored in a charge set named according to the input file, and marked by ''ref''. All charge sets are available for analysis in the other tabs of the '''Specifics page'''.		Note that multiple ''jobs'' may have been run for this molecule. A job is defined based on the molecule and its total charge, along with the EEM parameter set and computation method used. Each job produces a distinct ''set of charges'' with a unique ID encoding the EEM parameter set, method and total molecular charge. If the original input file contained values of atomic charges, these are also stored in a charge set named according to the input file, and marked by ''ref''. All charge sets are available for analysis in the other tabs of the '''Specifics page'''.

	Warnings and errors generated while processing the input files and running the calculation are listed in the right panel of the '''Summary tab'''. Each job will have its own list of errors and warnings. Jobs with errors generally do not produce any charge set, while jobs with warnings do. Warnings inform about some action taken under unexpected circumstances (e.g, defaulting to different parameters for certain atoms), or draw attention to aspects which may represent issues (e.g., ~~insufficient number of~~ H ~~to satisfy all valences~~).		Warnings and errors generated while processing the input files and running the calculation are listed in the right panel of the '''Summary tab'''. Each job will have its own list of errors and warnings. Jobs with errors generally do not produce any charge set, while jobs with warnings do. Warnings inform about some action taken under unexpected circumstances (e.g, defaulting to different parameters for certain atoms), or draw attention to aspects which may represent issues (e.g., missing H atoms).

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Crina: /* Synopsis page */

2015-03-03T22:12:45Z

Synopsis page

← Older revision		Revision as of 22:12, 3 March 2015
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	=Synopsis page=		=Synopsis page=

	The '''ACC Synopsis page''' contains an overview of your computation, which might have consisted of multiple jobs for multiple molecules. You may download all the results now ~~(molecular structure files containing atomic charges, statistics of the results, information about all jobs)~~, or return to this page later via this URL. You may also inspect the results directly in your web browser.		The '''ACC Synopsis page''' contains an overview of your computation, which might have consisted of multiple jobs for multiple molecules. You may download all the results now, or return to this page later via this URL. You may also inspect the results directly in your web browser.

			ACC downloadable results consist of molecular structure files containing atomic charges (.mol2 and .pqr formats), statistics of the results (atomic charges, correlations between sets of charges from different jobs), information about all jobs (setup, run time, warnings, errors). Note that if EEM parameters were missing for some atoms, the charge for these atoms will appear as 0.000 in the .mol2 and .pqr files, and as "-" in the .csv files. The .wprop files will not list these atoms at all.

	For each molecule, the table lists the number of atoms and chemical formula, the time it took '''ACC''' to complete all jobs pertaining to that molecule, along with the number of warnings and errors it encountered. Note that the timing listed by '''ACC''' for the first molecule in the table is actually the total computation time for all molecules, and thus it may seem disproportionately large compared to the timing listed for each of the remaining molecules in the table.		For each molecule, the table lists the number of atoms and chemical formula, the time it took '''ACC''' to complete all jobs pertaining to that molecule, along with the number of warnings and errors it encountered. Note that the timing listed by '''ACC''' for the first molecule in the table is actually the total computation time for all molecules, and thus it may seem disproportionately large compared to the timing listed for each of the remaining molecules in the table.

Crina: /* Raw Data */

2015-03-03T22:01:12Z

Raw Data

← Older revision		Revision as of 22:01, 3 March 2015
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	[[File:ACC_FirstTimeUserGuide 15.jpg\|thumb\|right\|650px\| The '''Raw Data tab''' allows to view the values of atomic or residue charges, depending on the ''Atom Grouping'' menu. Each column shows charges resulted from a single job, or read from the input file. The filter works on the atom or residue labels, and can parse regular expressions.]]		[[File:ACC_FirstTimeUserGuide 15.jpg\|thumb\|right\|650px\| The '''Raw Data tab''' allows to view the values of atomic or residue charges, depending on the ''Atom Grouping'' menu. Each column shows charges resulted from a single job, or read from the input file. The filter works on the atom or residue labels, and can parse regular expressions.]]

	The ''raw data'' is available in tabular form, and refers to the actual values of atomic charges resulted from the EEM calculation, or read in from the input file. Residue charges are also available if residue annotations are available in the input file. No additional statistics are included here.		The ''raw data'' is available in tabular form, and refers to the actual values of atomic charges resulted from the EEM calculation, or read in from the input file. Residue charges are also available if residue annotations are available in the input file. No additional statistics are included here. Note that if EEM parameters were missing for some atoms, the charge for these atoms will appear here as "n/a". The same is true for residues made up only of such atoms, namely their total charge will be "n/a".

	'''ACC''' allows access to the raw data at more levels of resolution (''atom grouping''). In the ''Atom Grouping'' menu, pick ''Atoms'' to list atomic charges, or ''Residues'' to list residue charges (sum of atomic charges for each residue).		'''ACC''' allows access to the raw data at more levels of resolution (''atom grouping''). In the ''Atom Grouping'' menu, pick ''Atoms'' to list atomic charges, or ''Residues'' to list residue charges (sum of atomic charges for each residue).

Lukas at 10:06, 28 December 2014

2014-12-28T10:06:57Z

← Older revision		Revision as of 10:06, 28 December 2014
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	In the table with molecules, click on a molecule name (Id) to visualize and analyze the results for this molecule in detail. Each [[ChargeCalculator:Terminology#Molecule \| ''molecule'']] is identified according to the name of the input file, and comprises all structural elements in the input file, from simple compounds to biomacromolecular complexes made up of proteins, nucleic acids, ligands, ions, water, etc. For each molecule, your computation may have consisted of several [[ChargeCalculator:Terminology#Molecule \| ''jobs'']], in which case all the results will be available for analysis.		In the table with molecules, click on a molecule name (Id) to visualize and analyze the results for this molecule in detail. Each [[ChargeCalculator:Terminology#Molecule \| ''molecule'']] is identified according to the name of the input file, and comprises all structural elements in the input file, from simple compounds to biomacromolecular complexes made up of proteins, nucleic acids, ligands, ions, water, etc. For each molecule, your computation may have consisted of several [[ChargeCalculator:Terminology#Molecule \| ''jobs'']], in which case all the results will be available for analysis.

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	\|<!--Col1-->[[File:ACC FirstTimeUserGuide 12.jpg\| 650px]]		\|<!--Col1-->[[File:ACC FirstTimeUserGuide 12.jpg\| 650px]]

Crina: /* 3D Model */

2014-12-16T17:12:41Z

3D Model

← Older revision		Revision as of 17:12, 16 December 2014
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	[[File:ACC FirstTimeUserGuide 19.jpg\|thumb\|right\|650px\| To find out what the ~~settings~~ mean~~, why they are required and how they influence your calculation~~, take advantage of all the help available as interactive guides and tool tips. ]]		[[File:ACC FirstTimeUserGuide 19.jpg\|thumb\|right\|650px\| To find out what the display and analysis options mean, take advantage of all the help available as interactive guides and tool tips. ]]

	Finally, if you don't know what something means or how it works, don't forget that there is plenty of help available directly on the '''ACC''' web pages. Hover the mouse over any keyword you do not understand to reveal a useful tool tip. Click on any of the buttons marking the interactive guides. Note that such guides are available for the entire '''Results page''', and for any of the tabs on the '''Specifics page'''.		Finally, if you don't know what something means or how it works, don't forget that there is plenty of help available directly on the '''ACC''' web pages. Hover the mouse over any keyword you do not understand to reveal a useful tool tip. Click on any of the buttons marking the interactive guides. Note that such guides are available for the entire '''Results page''', and for any of the tabs on the '''Specifics page'''.

Crina: /* 3D Model */

2014-12-16T17:11:42Z

3D Model

← Older revision		Revision as of 17:11, 16 December 2014
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	[[File:ACC FirstTimeUserGuide 19.jpg\|thumb\|right\|650px\| ]]		[[File:ACC FirstTimeUserGuide 19.jpg\|thumb\|right\|650px\| To find out what the settings mean, why they are required and how they influence your calculation, take advantage of all the help available as interactive guides and tool tips. ]]

			Finally, if you don't know what something means or how it works, don't forget that there is plenty of help available directly on the '''ACC''' web pages. Hover the mouse over any keyword you do not understand to reveal a useful tool tip. Click on any of the buttons marking the interactive guides. Note that such guides are available for the entire '''Results page''', and for any of the tabs on the '''Specifics page'''.


	'''The complete list of keywords involved in the interpretation of ACC results is available in the [[ChargeCalculator:Index \| Index]].'''		'''The complete list of keywords involved in the interpretation of ACC results is available in the [[ChargeCalculator:Index \| Index]].'''
	'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''		'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''

Crina: /* 3D Model */

2014-12-16T17:09:17Z

3D Model

← Older revision		Revision as of 17:09, 16 December 2014
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	<br style="clear:both" />		<br style="clear:both" />

			[[File:ACC FirstTimeUserGuide 19.jpg\|thumb\|right\|650px\| ]]



	'''The complete list of keywords involved in the interpretation of ACC results is available in the [[ChargeCalculator:Index \| Index]].'''		'''The complete list of keywords involved in the interpretation of ACC results is available in the [[ChargeCalculator:Index \| Index]].'''
	'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''		'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''

Crina: /* 3D Model */

2014-12-16T17:06:17Z

3D Model

← Older revision		Revision as of 17:06, 16 December 2014
Line 83:		Line 83:

	==3D Model==		==3D Model==
	[[File:ACC FirstTimeUserGuide 17.jpg\|thumb\|right\|650px\| The '''3D Model tab''' displays a 3D model of your molecule, based either on atomic or residue resolution. The contents of the visualization window are dictated by the panel on the left.]]		[[File:ACC FirstTimeUserGuide 18.jpg\|thumb\|right\|650px\| The '''3D Model tab''' displays a 3D model of your molecule, based either on atomic or residue resolution. The contents of the visualization window are dictated by the panel on the left.]]

	'''ACC''' allows a few basic charge visualization options to aid in interpreting the results of the atomic charge calculation. You may need to update your browser and driver version to be able to run the 3D visualizer (see the [[ChargeCalculator:Technical_details#Requirements \| requirements]]). The panels on the left dictate contents of the visualization window on the right, which allows you to display and manipulate with a ''3D model of your molecule colored according to charges''. The legend for mouse controls for manipulating with the 3D model (rotation, zoom) is available in the right bottom corner of the visualization window.		'''ACC''' allows a few basic charge visualization options to aid in interpreting the results of the atomic charge calculation. You may need to update your browser and driver version to be able to run the 3D visualizer (see the [[ChargeCalculator:Technical_details#Requirements \| requirements]]). The panels on the left dictate contents of the visualization window on the right, which allows you to display and manipulate with a ''3D model of your molecule colored according to charges''. The legend for mouse controls for manipulating with the 3D model (rotation, zoom) is available in the right bottom corner of the visualization window.

Crina: /* Compare */

2014-12-16T17:06:06Z

Compare

← Older revision		Revision as of 17:06, 16 December 2014
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	==Compare==		==Compare==
	[[File:ACC FirstTimeUserGuide 16.jpg\|thumb\|right\|650px\| The '''Compare tab''' allows to compare atomic or residue charges resulted from different jobs, or read from the input file. The contents of the graph are dictated by the panel on the left.]]		[[File:ACC FirstTimeUserGuide 17.jpg\|thumb\|right\|650px\| The '''Compare tab''' allows to compare atomic or residue charges resulted from different jobs, or read from the input file. The contents of the graph are dictated by the panel on the left.]]

	'''ACC''' allows to compare sets of charges at more levels of resolution, in graphical and tabular form. These sets of charges may have resulted from different jobs, or were read from the input file.		'''ACC''' allows to compare sets of charges at more levels of resolution, in graphical and tabular form. These sets of charges may have resulted from different jobs, or were read from the input file.