Praktikum Biophysikalische Chemie - Revision history

141.2.22.224: /* Write the NOE distance restraint file */

2009-01-13T08:33:58Z

Write the NOE distance restraint file

← Older revision		Revision as of 10:33, 13 January 2009
Line 70:		Line 70:

	Residue and atom names are given in upper case letters. The exact number of spaces between different items is irrelevant, but the "TAB" key should not be used.		Residue and atom names are given in upper case letters. The exact number of spaces between different items is irrelevant, but the "TAB" key should not be used.

	~~Note that the backbone amide hydrogen is called "H", not "HN".~~

	Degenerate groups of atoms, e.g. methyl groups, and diastereotopic pairs of hydrogen atoms, e.g. HB2/HB3 in serine, are referred to by "pseudoatoms" whose names are derived from the names of the hydrogen atoms that they represent by changing the first letter from "H" to "Q" and omitting the last digit. For instance, "HB2" and "HB3" are represented by a pseudoatom called "QB".		Degenerate groups of atoms, e.g. methyl groups, and diastereotopic pairs of hydrogen atoms, e.g. HB2/HB3 in serine, are referred to by "pseudoatoms" whose names are derived from the names of the hydrogen atoms that they represent by changing the first letter from "H" to "Q" and omitting the last digit. For instance, "HB2" and "HB3" are represented by a pseudoatom called "QB".

141.2.137.254: /* Analyze the results of the structure calculation */

2009-01-12T14:24:06Z

Analyze the results of the structure calculation

← Older revision		Revision as of 16:24, 12 January 2009
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	Upper QB LEU 17 - QB PRO 108 3.69 3 0.10 0.50 ++ * peak 1009		Upper QB LEU 17 - QB PRO 108 3.69 3 0.10 0.50 ++ * peak 1009
	Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.37 +++*++++++ peak 803		Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.37 +++*++++++ peak 803
	~~VdW N LEU 39 - CD1 LEU 39 3.05 10 0.23 0.24 ++++*+++++~~
	~~VdW N ILE 81 - CD PRO 82 3.05 10 0.26 0.29 ++++*+++++~~
	VdW N ILE 81 - HD2 PRO 82 2.45 10 0.34 0.37 ++++*+++++		VdW N ILE 81 - HD2 PRO 82 2.45 10 0.34 0.37 ++++*+++++
	VdW CG2 ILE 81 - C ILE 81 2.90 6 0.20 0.21 + + ++* +		VdW CG2 ILE 81 - C ILE 81 2.90 6 0.20 0.21 + + ++* +
	~~VdW CB THR 91 - H GLN 92 2.55 7 0.22 0.28 ++*+ +++~~
	~~VdW O THR 91 - CB GLN 92 2.90 3 0.16 0.20 *+ +~~
	~~VdW HA VAL 107 - CD PRO 108 2.60 5 0.19 0.27 +* ++ +~~
	2 violated distance restraints.		2 violated distance restraints.
	0 violated angle restraints.		0 violated angle restraints.

141.2.137.254: /* Write the initialization script */

2009-01-12T11:55:43Z

Write the initialization script

← Older revision		Revision as of 13:55, 12 January 2009
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	read seq vaso.seq		read seq vaso.seq
	library rename H atom=HN		library rename H atom=HN
			rmsdrange:=1-6

	These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq vaso.seq''' reads the polypeptide sequence. The ~~last~~ command, '''library rename''', changes the name of the backbone hydrogen atom from "H" to "HN".		These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq vaso.seq''' reads the polypeptide sequence. The command '''library rename H atom=HN''' changes the name of the backbone hydrogen atom from "H" to "HN". The variable '''rmsdrange''' is set to the preferred residue range for RMSD calculation.

	=== Write the NOE distance restraint file ===		=== Write the NOE distance restraint file ===

141.2.137.254: /* Write the initialization script */

2009-01-12T11:54:03Z

Write the initialization script

← Older revision		Revision as of 13:54, 12 January 2009
Line 37:		Line 37:
	library rename H atom=HN		library rename H atom=HN

	These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq vaso.seq''' reads the polypeptide sequence. The last command, '''library rename''' changes the name of the backbone hydrogen atom from "H" to "HN".		These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq vaso.seq''' reads the polypeptide sequence. The last command, '''library rename''', changes the name of the backbone hydrogen atom from "H" to "HN".

	=== Write the NOE distance restraint file ===		=== Write the NOE distance restraint file ===

141.2.137.254: /* Write the initialization script */

2009-01-12T11:53:49Z

Write the initialization script

← Older revision		Revision as of 13:53, 12 January 2009
Line 35:		Line 35:
	cyanalib		cyanalib
	read seq vaso.seq		read seq vaso.seq
			library rename H atom=HN

	These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq vaso.seq''' reads the polypeptide sequence.		These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq vaso.seq''' reads the polypeptide sequence. The last command, '''library rename''' changes the name of the backbone hydrogen atom from "H" to "HN".

	=== Write the NOE distance restraint file ===		=== Write the NOE distance restraint file ===

141.2.137.254: /* Startup */

2009-01-12T10:26:34Z

Startup

← Older revision		Revision as of 12:26, 12 January 2009
Line 8:		Line 8:

	bash		bash
	. /usr/local/courseexchange/~~setup_cyana~~.sh		. /usr/local/courseexchange/cyana_setup.sh

	Create a new directory, '''vaso''', for the structure calculation, and change into it:		Create a new directory, '''vaso''', for the structure calculation, and change into it:

141.2.137.254: /* Analyze the results of the structure calculation */

2009-01-12T10:22:02Z

Analyze the results of the structure calculation

← Older revision		Revision as of 12:22, 12 January 2009
Line 146:		Line 146:

	Constraints violated in 3 or more structures:		Constraints violated in 3 or more structures:
	# mean max. 1 5 10		# mean max. 1 5 10
	Upper QB LEU 17 - QB PRO 108 3.69 3 0.10 0.50 ++ * peak 1009		Upper QB LEU 17 - QB PRO 108 3.69 3 0.10 0.50 ++ * peak 1009
	Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.37 +++*++++++ peak 803		Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.37 +++*++++++ peak 803

141.2.137.254: /* Analyze the results of the structure calculation */

2009-01-12T10:21:16Z

Analyze the results of the structure calculation

← Older revision		Revision as of 12:21, 12 January 2009
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	* the rank of the structure sorted by target function value		* the rank of the structure sorted by target function value
	* the target function value		* the target function value
	* three columns for each type of conformational restraints ~~that is present~~:		* three columns for each type of conformational restraints:
	** the number of restraints that are violated by more than the cutoff value given in the last row (“Cut”)		** the number of restraints that are violated by more than the cutoff value given in the last row (“Cut”)
	** the root-mean-square (RMS) violation calculated over all, violated and fulfilled, restraints of this type		** the root-mean-square (RMS) violation calculated over all, violated and fulfilled, restraints of this type

141.2.137.254: /* Analyze the results of the structure calculation */

2009-01-12T10:20:37Z

Analyze the results of the structure calculation

← Older revision		Revision as of 12:20, 12 January 2009
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	Average heavy atom RMSD to mean : 1.08 +/- 0.11 A (0.93..1.25 A; 10 structures)		Average heavy atom RMSD to mean : 1.08 +/- 0.11 A (0.93..1.25 A; 10 structures)

	The residue range used for the superposition is indicated~~, and~~ RMSD values are computed for the backbone and heavy atoms ~~with~~ the ~~rmsd command~~. The average value, the standard deviation, and the minimal and maximal values of the RMSDs between the analyzed structures and their mean coordinates are calculated.		The residue range used for the superposition is indicated. RMSD values are computed for the backbone and heavy atoms of the given residues. The average value, the standard deviation, and the minimal and maximal values of the RMSDs between the analyzed structures and their mean coordinates are calculated.

	=== Visualize the structure ===		=== Visualize the structure ===

141.2.137.254: /* Printing */

2009-01-12T10:18:58Z

Printing

← Older revision		Revision as of 12:18, 12 January 2009
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	=== Printing ===		=== Printing ===

	~~The~~ local printer can be accessed with the name '''bpc_lokal''' from Linux, or '''BPC HP Laser Jet 4250 PS''' from Windows XP.		A local printer can be accessed with the name '''bpc_lokal''' from Linux, or '''BPC HP Laser Jet 4250 PS''' from Windows XP.