DOCK Blaster:Progress Bar - Revision history

Therese: 8 revisions

2012-10-08T20:02:11Z

8 revisions

← Older revision

Revision as of 20:02, 8 October 2012

Frodo: /* Target Preparation */

2009-08-06T23:01:00Z

Target Preparation

← Older revision		Revision as of 23:01, 6 August 2009
Line 17:		Line 17:

	=== Queued (Q'd) ===		=== Queued (Q'd) ===
	Your job has been submitted to the queue, but has not yet started. It will start as soon as system capacity allows.		Your job has been submitted to the queue, but has not yet started. It will start as soon as system capacity allows. If the cluster is heavily loaded, you can potentially be stuck in this stage for a long time. We aim to give you useful guidance to help you manage your expectations.

	=== Running ===		=== Running ===
	Your job is running, or at least, it has not reported as having ended.		Your job is running, or at least, it has not reported as having ended. This stage typically takes 15 minutes, but can take an hour. If it takes much more than an hour then something has probably gone wrong.

	=== Done ===		=== Done ===
	Target preparation has ended normally. Normally, the calculation proceeds directly into calibration, so it is rare to be at this stage.		Target preparation has ended normally. Normally, the calculation proceeds directly into calibration, so it is rare to be at this stage.

	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]

Frodo: /* Calibration */

2009-08-06T22:59:03Z

Calibration

← Older revision		Revision as of 22:59, 6 August 2009
Line 28:		Line 28:

	= Calibration =		= Calibration =
	Calibration is the process of performing control calculations to investigate whether docking is ~~"working" against your target~~. ~~More info needed here~~.		Calibration is the process of performing control calculations to investigate whether docking can recapitulate known experimental information. DOCK Blaster tries two different sampling schemes and two different scoring schemes, much as an expert might do to explore the sensitivity of the calculation to the parameters used. If you supplied a docked ligand, such as a crystallographic ligand, or started from a PDB code, then the ligand is re-docked, and its rank is compared with about 100 property-matched decoys. If you supplied actives or inactives (optional), then these are docked, for comparison with the ligand and its decoys. In every case, two additional databases are always docked. These are extrema and random. Extrema are molecules with calculated LogP < -3 and molecular weight less than 250. They are used to highlight possible weaknesses in docking calculation that would make it highly sensitive to charge. Random are about 200 molecules, quite diverse, that can be used to expose other weaknesses in the docking calculation prior to full database docking.

			Calibration can be in one of three states: Queued, Running, and Done.

	=== Queued ===		=== Queued ===
	Your calibration ~~jobs are~~ queued and will start when system resources ~~allow~~.		Your calibration calculation is queued and will start when system resources permit. If the cluster is heavily loaded, you can potentially be stuck in this stage for a long time. We will try to provide timely information to help you manage your expectations.

	=== Running ===		=== Running ===
	Your calibration jobs are running.		Your calibration jobs are running. Typically, this should take a few minutes - in unusual cases an hour. If it takes much more than an hour something has probably gone wrong.


	=== Done ===		=== Done ===
	Your calibration ~~jobs have~~ ended. ~~This is~~ the ~~stage where your input~~ is ~~required~~, ~~prior to full database docking~~. ~~View~~ the ~~calibration results~~, ~~pick~~ the ~~best conditions~~, ~~satisfy yourself that docking~~ is ~~working~~, ~~and~~ then ~~launch a~~ database ~~docking job~~.		Your calibration calculation has ended. At this point, the preliminary docking results should be evaluated with the goal of deciding whether prospective database screening is warranted.

			If you supplied a ligand, you will be presented with a Preliminary Docking Results table. Good results are indicated in green, borderline results in yellow, and poor results in red. If the calculation did not complete an uncolored error message will indicate this.

			We recommend always looking closely at the ligand and its decoys, which you can do blah blah blah. If you are satisfied with the ligand poses, and if the color is green, then we recommend prospective database screening.

			MORE HERE


			[[Category:DOCK Blaster]]

	= Docking =		= Docking =

Frodo: /* Target Preparation */

2009-08-06T22:48:44Z

Target Preparation

← Older revision		Revision as of 22:48, 6 August 2009
Line 14:		Line 14:

	= Target Preparation =		= Target Preparation =
	This ~~is the~~ stage ~~where we process your uploaded files, preparing~~ hot spots and ~~precalculating~~ scoring grids. We also ~~prepare any~~ libraries of compounds for calibration calculations. There are three stages of target preparation.		This stage prepares "hot spots" (aka "orientation spheres") and precalculates scoring grids. It also prepares libraries of compounds for calibration calculations. There are three sub-stages of target preparation: Queued, Running, and Done.

	=== Queued (Q'd) ===		=== Queued (Q'd) ===
	Your job has been submitted to the ~~server~~, but has not yet started. It will start as soon as system ~~limits allow~~.		Your job has been submitted to the queue, but has not yet started. It will start as soon as system capacity allows.

	=== Running ===		=== Running ===
	Your job is running.		Your job is running, or at least, it has not reported as having ended.

	=== Done ===		=== Done ===
	Target preparation has ended normally. ~~Usually~~, ~~we go straight~~ into calibration, so ~~you may never see~~ this stage.		Target preparation has ended normally. Normally, the calculation proceeds directly into calibration, so it is rare to be at this stage.

			[[Category:DOCK Blaster]]

	= Calibration =		= Calibration =

Frodo at 22:44, 6 August 2009

2009-08-06T22:44:49Z

← Older revision		Revision as of 22:44, 6 August 2009
Line 1:		Line 1:
	The DOCK Blaster Progress Bar tells you where you are in the docking pipeline.		The DOCK Blaster Progress Bar tells you where you are in the docking pipeline by coloring your current stage in yellow.

	[[Image:Nav1.png]]		[[Image:Nav1.png]]

JohnIrwin at 05:16, 4 October 2007

2007-10-04T05:16:44Z

← Older revision		Revision as of 05:16, 4 October 2007
Line 4:		Line 4:

	There are six stages, some with several substages, as follows: Preparer, Scrutinizer, Target Preparation, Calibration, Docking, and Results.		There are six stages, some with several substages, as follows: Preparer, Scrutinizer, Target Preparation, Calibration, Docking, and Results.
			{{TOCright}}
	= Preparer =		= Preparer =
	The preparer assists you in preparing a job. Here you upload your data to the DOCK Blaster server. For more information about the data formats, please see [[DOCK Blaster:Prepare Input \| Prepare Input]].		The preparer assists you in preparing a job. Here you upload your data to the DOCK Blaster server. For more information about the data formats, please see [[DOCK Blaster:Prepare Input \| Prepare Input]].

JohnIrwin at 05:15, 4 October 2007

2007-10-04T05:15:11Z

← Older revision		Revision as of 05:15, 4 October 2007
Line 3:		Line 3:
	[[Image:Nav1.png]]		[[Image:Nav1.png]]

	There are six stages ~~and~~ several substages as follows.		There are six stages, some with several substages, as follows: Preparer, Scrutinizer, Target Preparation, Calibration, Docking, and Results.

	== Preparer ==		= Preparer =
	~~This is where~~ you upload your data to the DOCK Blaster server. For more information about the data formats, please see [[DOCK Blaster:Prepare Input]].		The preparer assists you in preparing a job. Here you upload your data to the DOCK Blaster server. For more information about the data formats, please see [[DOCK Blaster:Prepare Input \| Prepare Input]].


	== Scrutinizer ==		= Scrutinizer =
	This is the page you see immediately after pressing the "DOCK" button. Your data are uploaded to the server, and the Scrutinizer checks the data for consistency. For more information about the Scrutinizer, and the many ways it can complain about your data, please see [[DOCK Blaster:Scrutinizer]].		This is the page you see immediately after pressing the "DOCK" button. Your data are uploaded to the server, and the Scrutinizer checks the data for consistency. For more information about the Scrutinizer, and the many ways it can complain about your data, please see [[DOCK Blaster:Scrutinizer \| Scrutinizer]].


	== Target Preparation ==		= Target Preparation =
	This is the stage where we process your uploaded files, preparing hot spots and precalculating scoring grids. We also prepare any libraries of compounds for calibration calculations. There are three stages of target preparation.		This is the stage where we process your uploaded files, preparing hot spots and precalculating scoring grids. We also prepare any libraries of compounds for calibration calculations. There are three stages of target preparation.

Line 26:		Line 26:


	== Calibration ==		= Calibration =
	Calibration is the process of performing control calculations to investigate whether docking is "working" against your target. More info needed here.		Calibration is the process of performing control calculations to investigate whether docking is "working" against your target. More info needed here.

Line 40:		Line 40:


	== Docking ==		= Docking =
	This is when real database docking is done.		This is when real database docking is done.

Line 50:		Line 50:


	== Results ==		= Results =
	Your docking jobs have ended.		Your docking jobs have ended.
	You may now look at the results.		You may now look at the results.

JohnIrwin at 18:16, 21 September 2007

2007-09-21T18:16:31Z

← Older revision		Revision as of 18:16, 21 September 2007
Line 53:		Line 53:
	Your docking jobs have ended.		Your docking jobs have ended.
	You may now look at the results.		You may now look at the results.


			[[Category:DOCK Blaster]]
			[[Category:GUI]]
			[[Category:Manual]]

JohnIrwin at 19:14, 19 March 2007

2007-03-19T19:14:51Z

New page

The DOCK Blaster Progress Bar tells you where you are in the docking pipeline.

[[Image:Nav1.png]]

There are six stages and several substages as follows.

== Preparer ==
This is where you upload your data to the DOCK Blaster server. For more information about the data formats, please see [[DOCK Blaster:Prepare Input]].

== Scrutinizer ==
This is the page you see immediately after pressing the "DOCK" button. Your data are uploaded to the server, and the Scrutinizer checks the data for consistency. For more information about the Scrutinizer, and the many ways it can complain about your data, please see [[DOCK Blaster:Scrutinizer]].

== Target Preparation ==
This is the stage where we process your uploaded files, preparing hot spots and precalculating scoring grids. We also prepare any libraries of compounds for calibration calculations. There are three stages of target preparation.

=== Queued (Q'd) ===
Your job has been submitted to the server, but has not yet started. It will start as soon as system limits allow.

=== Running ===
Your job is running.

=== Done ===
Target preparation has ended normally. Usually, we go straight into calibration, so you may never see this stage.

== Calibration ==
Calibration is the process of performing control calculations to investigate whether docking is "working" against your target. More info needed here.

=== Queued ===
Your calibration jobs are queued and will start when system resources allow.

=== Running ===
Your calibration jobs are running.

=== Done ===
Your calibration jobs have ended. This is the stage where your input is required, prior to full database docking. View the calibration results, pick the best conditions, satisfy yourself that docking is working, and then launch a database docking job.

== Docking ==
This is when real database docking is done.

=== Queued ===
Your docking job is queued.

=== Running ===
Your docking jobs are running.

== Results ==
Your docking jobs have ended.
You may now look at the results.