Automated resonance assignment with FLYA (EMBO 2013) - Revision history

Guentert: moved Automated resonance assignment with FLYA to Automated resonance assignment with FLYA (EMBO 2013)

2014-10-13T20:37:54Z

← Older revision	Revision as of 22:37, 13 October 2014
(No difference)

2013-07-29T08:10:45Z

← Older revision		Revision as of 10:10, 29 July 2013
Line 1:		Line 1:
	In this tutorial we want to determine the resonance assignments and the structure of a protein using the program CYANA.		In this tutorial we want to determine the resonance assignments and the structure of a protein using the program CYANA.


	== CYANA setup for the EMBO Practical Course NMR in Basel (20–27 July 2013) ==		== CYANA setup for the EMBO Practical Course NMR in Basel (20–27 July 2013) ==

2013-07-29T08:10:23Z

← Older revision		Revision as of 10:10, 29 July 2013
Line 1:		Line 1:
	In this tutorial we want to determine the resonance assignments and the structure of a protein using the program CYANA.		In this tutorial we want to determine the resonance assignments and the structure of a protein using the program CYANA.


	== CYANA setup for the EMBO Practical Course NMR in Basel (20–27 July 2013) ==		== CYANA setup for the EMBO Practical Course NMR in Basel (20–27 July 2013) ==

2013-07-29T08:09:17Z

FLYA initialization script

← Older revision		Revision as of 10:09, 29 July 2013
Line 87:		Line 87:
	The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros".		The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros".

	One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library and the protein sequence:		One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any time one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library and the protein sequence:

	cyanalib		cyanalib

2013-07-22T14:19:12Z

← Older revision		Revision as of 16:19, 22 July 2013
Line 37:		Line 37:
	If you want to return to your practical later, using your own Linux or Mac OS X computer, you can download the demo version of CYANA from [[Media:cyana-3.96bin-130719demo.tgz‎\|here]]. ''This is not necessary on the workshop computers where the software is already installed.''		If you want to return to your practical later, using your own Linux or Mac OS X computer, you can download the demo version of CYANA from [[Media:cyana-3.96bin-130719demo.tgz‎\|here]]. ''This is not necessary on the workshop computers where the software is already installed.''

	Hint: More information on the CYANA commands etc. is in the [[CYANA 3.0 Reference Manual]].		'''Hint:''' More information on the CYANA commands etc. is in the [[CYANA 3.0 Reference Manual]].

	== Experimental input data ==		== Experimental input data ==

2013-07-22T14:18:40Z

CYANA setup for the EMBO Practical Course NMR in Basel (20–27 July 2013)

← Older revision		Revision as of 16:18, 22 July 2013
Line 36:		Line 36:

	If you want to return to your practical later, using your own Linux or Mac OS X computer, you can download the demo version of CYANA from [[Media:cyana-3.96bin-130719demo.tgz‎\|here]]. ''This is not necessary on the workshop computers where the software is already installed.''		If you want to return to your practical later, using your own Linux or Mac OS X computer, you can download the demo version of CYANA from [[Media:cyana-3.96bin-130719demo.tgz‎\|here]]. ''This is not necessary on the workshop computers where the software is already installed.''

			Hint: More information on the CYANA commands etc. is in the [[CYANA 3.0 Reference Manual]].

	== Experimental input data ==		== Experimental input data ==

2013-07-22T14:17:21Z

Fully automated structure calculation

← Older revision		Revision as of 16:17, 22 July 2013
Line 357:		Line 357:

	molmol -r 8-110 final.pdb		molmol -r 8-110 final.pdb

			The optimal residue range for superposition can be found with the command

			cyana overlay final.pdb

			or with the [http://www.bpc.uni-frankfurt.de/cyrange.html CYRANGE web server].

	=== Download results of fully automated structure calculation ===		=== Download results of fully automated structure calculation ===

	If you cannot complete the fully automated structure calculation but want to look at the results that have been calculated previously, you may download them [[Media:flyaemboresults.tgz\|here]] (about 24 MB).		If you cannot complete the fully automated structure calculation but want to look at the results that have been calculated previously, you may download them [[Media:flyaemboresults.tgz\|here]] (about 24 MB).

2013-07-22T14:07:22Z

Download results of fully automated structure calculation

← Older revision		Revision as of 16:07, 22 July 2013
Line 360:		Line 360:
	=== Download results of fully automated structure calculation ===		=== Download results of fully automated structure calculation ===

	If you cannot complete the fully automated structure calculation but want to look at the results ~~tht~~ have been ~~calculate~~ previously, you may download them [[Media:flyaemboresults.tgz\|here]] (about 24 MB).		If you cannot complete the fully automated structure calculation but want to look at the results that have been calculated previously, you may download them [[Media:flyaemboresults.tgz\|here]] (about 24 MB).

2013-07-22T14:04:48Z

Download results of fully automated structure calculation

← Older revision		Revision as of 16:04, 22 July 2013
Line 360:		Line 360:
	=== Download results of fully automated structure calculation ===		=== Download results of fully automated structure calculation ===

	If you cannot complete the fully automated structure calculation but want to look at the results tht have been calculate previously, you may download them [[Media:flyaemboresults.tgz\|here]]~~here~~.		If you cannot complete the fully automated structure calculation but want to look at the results tht have been calculate previously, you may download them [[Media:flyaemboresults.tgz\|here]] (about 24 MB).

2013-07-22T14:03:51Z

Download results of fully automated structure calculation

← Older revision		Revision as of 16:03, 22 July 2013
Line 360:		Line 360:
	=== Download results of fully automated structure calculation ===		=== Download results of fully automated structure calculation ===

	If you cannot complete the fully automated structure calculation but want to look at the results tht have been calculate previously, you may download them here.		If you cannot complete the fully automated structure calculation but want to look at the results tht have been calculate previously, you may download them [[Media:flyaemboresults.tgz\|here]]here.