DOCK Blaster:Failure with PDB code - Revision history

Therese: 4 revisions

2012-10-08T20:02:08Z

4 revisions

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Revision as of 20:02, 8 October 2012

Frodo at 17:21, 1 September 2009

2009-09-01T17:21:15Z

← Older revision		Revision as of 17:21, 1 September 2009
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	Unfortunately, we were unable to run your DOCK Blaster job starting from a PDB code alone.		Unfortunately, we were unable to run your DOCK Blaster job starting from a PDB code alone.

	NOHETATMFOUND ~~- this~~ indicates that we could not automatically find a ligand to use to identify the binding site, and to use as a control for automated docking.		== NOHETATMFOUND ==

			This message indicates that we could not automatically find a ligand to use to identify the binding site, and to use as a control for automated docking.

	In the future, we may use automatic binding site identification software in this case. For now, if you know where the binding site on this protein is,l you may be able to rescue this case. Please use the "start with a structure" entry point into DOCK Blaster.		In the future, we may use automatic binding site identification software in this case. For now, if you know where the binding site on this protein is,l you may be able to rescue this case. Please use the "start with a structure" entry point into DOCK Blaster.
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	* Step 3. Scrape/copy these three residues into a file. Call the file "bindingsite.pdb". Now start DOCK Blaster using files.		* Step 3. Scrape/copy these three residues into a file. Call the file "bindingsite.pdb". Now start DOCK Blaster using files.
	* Step 4. If problems persist, please write us, quoting the final DOCK Blaster job ID number.		* Step 4. If problems persist, please write us, quoting the final DOCK Blaster job ID number.

			== Other problems ==
			In addition to "no atoms found", there may be more than one ligand. In this case, we should give you a choice. For now, the approach is to enter the three letter code of the ligand you want to use in the Parser, in addition to the PDB code.

			Good luck!



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

Frodo at 17:19, 1 September 2009

2009-09-01T17:19:54Z

← Older revision		Revision as of 17:19, 1 September 2009
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	Unfortunately, we were unable to run your DOCK Blaster job starting from a PDB code alone.		Unfortunately, we were unable to run your DOCK Blaster job starting from a PDB code alone.

	~~Here is where~~ we ~~provide more information about what may have gone wrong~~.		NOHETATMFOUND - this indicates that we could not automatically find a ligand to use to identify the binding site, and to use as a control for automated docking.

			In the future, we may use automatic binding site identification software in this case. For now, if you know where the binding site on this protein is,l you may be able to rescue this case. Please use the "start with a structure" entry point into DOCK Blaster.

			* Step 1. Download the PDB file.
			* Step 2. Identify the binding site. Pick 3 residues that triangulate the binding site. They do not have to be involved in the catalytic process, but the center of mass of these three residues should be where you want the ligand to go.
			* Step 3. Scrape/copy these three residues into a file. Call the file "bindingsite.pdb". Now start DOCK Blaster using files.
			* Step 4. If problems persist, please write us, quoting the final DOCK Blaster job ID number.


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

Frodo: Failure with PDB code moved to DOCK Blaster:Failure with PDB code: consistent naming

2009-08-10T19:14:07Z

Failure with PDB code moved to DOCK Blaster:Failure with PDB code: consistent naming

← Older revision

Revision as of 19:14, 10 August 2009

Frodo at 19:12, 10 August 2009

2009-08-10T19:12:03Z

New page

Unfortunately, we were unable to run your DOCK Blaster job starting from a PDB code alone.

Here is where we provide more information about what may have gone wrong.

[[Category:DOCK Blaster]]