CYANA Command: library check - Revision history

Masayo: /* Description */

2009-08-12T10:44:42Z

Description

← Older revision		Revision as of 12:44, 12 August 2009
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	== Description ==		== Description ==

	Checks the current residue library for inconsistencies. This command is also called implicitly when reading a residue library file with the '''read lib''' command. The following problems are reported:		Checks the current residue library for inconsistencies. This command is also called implicitly when reading a residue library file with the [[CYANA Commands: read lib\|'''read lib''']] command. The following problems are reported:

	* Duplicate residue names		* Duplicate residue names

Masayo: /* Description */

2009-08-07T08:30:47Z

Description

← Older revision		Revision as of 10:30, 7 August 2009
Line 6:		Line 6:
	== Description ==		== Description ==

	~~This command checks~~ the current residue library for		Checks the current residue library for inconsistencies. This command is also called implicitly when reading a residue library file with the '''read lib''' command. The following problems are reported:
	inconsistencies. This command is also called implicitly when reading
	a residue library file with the '''read lib''' command.

	The following problems are reported:

	* Duplicate residue names		* Duplicate residue names
Line 17:		Line 13:
	* Dihedral angles that affect preceding dihedral angles		* Dihedral angles that affect preceding dihedral angles

	The latter error occurs if the order of the dihedral angles and/or		The latter error occurs if the order of the dihedral angles and/or atoms within a residue is incorrect. To be compatible with the tree structure of dihedral angles, the dihedral angles and the atoms must be ordered according to two rules:
	atoms within a residue is incorrect. To be compatible with the tree
	structure of dihedral angles, the dihedral angles and the atoms must
	be ordered according to two rules:

	1. A change of a dihedral angle must not affect the		* A change of a dihedral angle must not affect the positions of the first, second, third, or forth atom in any preceding dihedral angle definition.
	positions of the first, second, third, or forth		* The set of atoms whose positions will be affected by a change of a dihedral angle consists of all atoms following the third atom in the dihedral angle definition up to the fifth (last) atom in the dihedral angle definition in the library, or the end of the main chain for backbone dihedral angles.
	atom in any preceding dihedral angle definition.
	2. The set of atoms whose positions will be affected
	by a change of a dihedral angle consists of all
	atoms following the third atom in the dihedral
	angle definition up to the fifth (last) atom in
	the dihedral angle definition in the library, or
	the end of the main chain for backbone dihedral
	angles.

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

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== Parameters ==

; (none)

== Description ==

This command checks the current residue library for
inconsistencies. This command is also called implicitly when reading
a residue library file with the '''read lib''' command.

The following problems are reported:

* Duplicate residue names
* Duplicate dihedral angle names
* Duplicate atom names
* Dihedral angles that affect preceding dihedral angles

The latter error occurs if the order of the dihedral angles and/or
atoms within a residue is incorrect. To be compatible with the tree
structure of dihedral angles, the dihedral angles and the atoms must
be ordered according to two rules:

1. A change of a dihedral angle must not affect the
positions of the first, second, third, or forth
atom in any preceding dihedral angle definition.
2. The set of atoms whose positions will be affected
by a change of a dihedral angle consists of all
atoms following the third atom in the dihedral
angle definition up to the fifth (last) atom in
the dihedral angle definition in the library, or
the end of the main chain for backbone dihedral
angles.