Defining non-standard residues - Revision history

Guentert at 16:08, 21 November 2024

2024-11-21T16:08:13Z

← Older revision		Revision as of 18:08, 21 November 2024
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	following two rules are fulfilled:		following two rules are fulfilled:

	* 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.		* A change of a dihedral angle must not affect the positions of the first, second, third, or fourth atom in any preceding dihedral angle definition.

	* 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 (or the end of the main chain for backbone dihedral angles).		* 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 (or the end of the main chain for backbone dihedral angles).

Guentert at 21:16, 17 August 2009

2009-08-17T21:16:23Z

← Older revision		Revision as of 23:16, 17 August 2009
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	* Check whether the angles and coordinates produced by the second run of CYANA coincide closely with those from the first run. If this test fails, then there is probably a format error in the new library entry or the ordering rules listed above are violated. However, this test does not detect errors in nomenclature, connectivities, or pointers to pseudo atoms.		* Check whether the angles and coordinates produced by the second run of CYANA coincide closely with those from the first run. If this test fails, then there is probably a format error in the new library entry or the ordering rules listed above are violated. However, this test does not detect errors in nomenclature, connectivities, or pointers to pseudo atoms.
	* Check the coordinates produced by CYANA on a molecular graphics system, for example with the program MOLMOL (Koradi et al., 1996).		* Check the coordinates produced by CYANA on a molecular graphics system, for example with the program MOLMOL (Koradi et al., 1996).

			== See also ==

			* [[Residue library file]]

Guentert: moved Using non-standard residues to Defining non-standard residues

2009-08-17T21:13:50Z

moved Using non-standard residues to Defining non-standard residues

← Older revision	Revision as of 23:13, 17 August 2009
(No difference)

Guentert at 21:08, 17 August 2009

2009-08-17T21:08:32Z

← Older revision		Revision as of 23:08, 17 August 2009
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	Non-standard residue types can be added to the residue library as additional		Non-standard residue types can be added to the residue library as additional
	entries. The procedure to add a new residue type to the library is		entries. The procedure to add a new residue type to the library is
	as follows (see ~~section “File formats” for a~~ description of the format of		as follows (see also the description of the format of
	the residue library file):		the [[residue library file]]):

	Create Cartesian coordinates for all atoms of the residue, for example		Create Cartesian coordinates for all atoms of the residue, for example

Guentert at 21:07, 17 August 2009

2009-08-17T21:07:08Z

← Older revision		Revision as of 23:07, 17 August 2009
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	new entry. These two steps are best done using the library format in		new entry. These two steps are best done using the library format in
	which connectivities and angle definitions are given by atom names rather		which connectivities and angle definitions are given by atom names rather
	than by atom numbers (see the option '''~~convert~~''' of the [[CYANA Command: write lib\|write lib]] command).		than by atom numbers (see the option '''names''' of the [[CYANA Command: write lib\|'''write lib''']] command).
	Make sure that the header line starting with RESIDUE is correct.		Make sure that the header line starting with RESIDUE is correct.
	Add the new entry to (a copy of) the residue library file. Test the new entry,		Add the new entry to (a copy of) the residue library file. Test the new entry,

Guentert at 21:06, 17 August 2009

2009-08-17T21:06:40Z

← Older revision		Revision as of 23:06, 17 August 2009
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	new entry. These two steps are best done using the library format in		new entry. These two steps are best done using the library format in
	which connectivities and angle definitions are given by atom names rather		which connectivities and angle definitions are given by atom names rather
	than by atom numbers (see the option '''convert''' of the [[CYANA Command: ~~read~~ lib\|~~read~~ lib]] command).		than by atom numbers (see the option '''convert''' of the [[CYANA Command: write lib\|write lib]] command).
	Make sure that the header line starting with RESIDUE is correct.		Make sure that the header line starting with RESIDUE is correct.
	Add the new entry to (a copy of) the residue library file. Test the new entry,		Add the new entry to (a copy of) the residue library file. Test the new entry,

Guentert at 21:06, 17 August 2009

2009-08-17T21:06:03Z

← Older revision		Revision as of 23:06, 17 August 2009
Line 27:		Line 27:
	new entry. These two steps are best done using the library format in		new entry. These two steps are best done using the library format in
	which connectivities and angle definitions are given by atom names rather		which connectivities and angle definitions are given by atom names rather
	than by atom numbers (see the option convert of the read lib command).		than by atom numbers (see the option '''convert''' of the [[CYANA Command: read lib\|read lib]] command).
	Make sure that the header line starting with RESIDUE is correct.		Make sure that the header line starting with RESIDUE is correct.
	Add the new entry to (a copy of) the residue library file. Test the new entry,		Add the new entry to (a copy of) the residue library file. Test the new entry,

Guentert at 21:05, 17 August 2009

2009-08-17T21:05:01Z

← Older revision		Revision as of 23:05, 17 August 2009
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	as follows (see section “File formats” for a description of the format of		as follows (see section “File formats” for a description of the format of
	the residue library file):		the residue library file):

	Create Cartesian coordinates for all atoms of the residue, for example		Create Cartesian coordinates for all atoms of the residue, for example
	with a molecular graphics program or using the attach and insert commands		with a molecular graphics program or using the attach and insert commands

Guentert at 21:03, 17 August 2009

2009-08-17T21:03:59Z

← Older revision		Revision as of 23:03, 17 August 2009
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	following two rules are fulfilled:		following two rules are fulfilled:

	* A change of a dihedral angle must not affect the positions of the first,		* 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.
	second, third, or forth atom in any preceding dihedral angle definition.

	* The set of atoms whose positions will be affected by a change of a		* 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 (or the end of the main chain for backbone dihedral angles).
	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 (or the end of the main chain for backbone dihedral angles).

	Convert the coordinates into the format of the library file (for example		Convert the coordinates into the format of the library file (for example
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	for example in the following way:		for example in the following way:

	* Create a sequence file that contains the new residue type, preferably		* Create a sequence file that contains the new residue type, preferably in the interior of the chain, i.e. not as the first or last residue.
	in the interior of the chain, i.e. not as the first or last residue.		* Using this sequence file and the new residue library in the program CYANA, create angle and coordinate files for a conformer with randomized dihedral angles.
	* Using this sequence file and the new residue library in the program		* Start CYANA again (with the same sequence and residue library file), read the previously produced coordinate file, and write again angle and coordinate files without making any minimization.
	CYANA, create angle and coordinate files for a conformer with randomized		* Check whether the angles and coordinates produced by the second run of CYANA coincide closely with those from the first run. If this test fails, then there is probably a format error in the new library entry or the ordering rules listed above are violated. However, this test does not detect errors in nomenclature, connectivities, or pointers to pseudo atoms.
	dihedral angles.		* Check the coordinates produced by CYANA on a molecular graphics system, for example with the program MOLMOL (Koradi et al., 1996).
	* Start CYANA again (with the same sequence and residue library file),
	read the previously produced coordinate file, and write again angle
	and coordinate files without making any minimization.
	* Check whether the angles and coordinates produced by the second
	run of CYANA coincide closely with those from the first run. If this
	test fails, then there is probably a format error in the new library entry
	or the ordering rules listed above are violated. However, this test
	does not detect errors in nomenclature, connectivities, or pointers to
	pseudo atoms.
	* Check the coordinates produced by CYANA on a molecular graphics
	system, for example with the program MOLMOL (Koradi et al.,
	1996).

Guentert: Created page with 'Non-standard residue types can be added to the residue library as additional entries. The procedure to add a new residue type to the library is as follows (see section “File fo…'

2009-08-17T21:02:54Z

Created page with 'Non-standard residue types can be added to the residue library as additional entries. The procedure to add a new residue type to the library is as follows (see section “File fo…'

New page

Non-standard residue types can be added to the residue library as additional
entries. The procedure to add a new residue type to the library is
as follows (see section “File formats” for a description of the format of
the residue library file):
Create Cartesian coordinates for all atoms of the residue, for example
with a molecular graphics program or using the attach and insert commands
of the program [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/COFIMA COFIMA].
Bond lengths, bond angles, and chiralities
of this structure must be correct but the conformation, i.e. the values
of the dihedral angles, does not matter. The coordinates of the overlap atoms
at the beginning and at the end of the residue (for example N, CA,
and C in amino acids) will also be needed. If the new residue type results
from a slight modification of an existing residue type, it is usually most
convenient to start from the coordinates of the existing residue type and
to modify them. Order the atoms such that their order is compatible with
the tree structure of dihedral angles that will be defined, i.e. such that the
following two rules are fulfilled:

* 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.

* 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 (or the end of the main chain for backbone dihedral angles).

Convert the coordinates into the format of the library file (for example
with a text editor). Add atom types, connectivities, and the information
about diastereotopic partners. Add the dihedral angle definitions to the
new entry. These two steps are best done using the library format in
which connectivities and angle definitions are given by atom names rather
than by atom numbers (see the option convert of the read lib command).
Make sure that the header line starting with RESIDUE is correct.
Add the new entry to (a copy of) the residue library file. Test the new entry,
for example in the following way:

* Create a sequence file that contains the new residue type, preferably
in the interior of the chain, i.e. not as the first or last residue.
* Using this sequence file and the new residue library in the program
CYANA, create angle and coordinate files for a conformer with randomized
dihedral angles.
* Start CYANA again (with the same sequence and residue library file),
read the previously produced coordinate file, and write again angle
and coordinate files without making any minimization.
* Check whether the angles and coordinates produced by the second
run of CYANA coincide closely with those from the first run. If this
test fails, then there is probably a format error in the new library entry
or the ordering rules listed above are violated. However, this test
does not detect errors in nomenclature, connectivities, or pointers to
pseudo atoms.
* Check the coordinates produced by CYANA on a molecular graphics
system, for example with the program MOLMOL (Koradi et al.,
1996).