Sequence file - Revision history

Admin: /* Basic format */

2009-01-29T12:58:47Z

Basic format

← Older revision		Revision as of 14:58, 29 January 2009
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	Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.		Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.

	By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, ω = 180° ~~<math>\omega = 180</math>~~. Optionally, OMEGA angles can be fixed in the ''cis'' position, ~~<math>\~~omega = ~~180</math>~~, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above.		By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, ''ω'' = 180°. Optionally, OMEGA angles can be fixed in the ''cis'' position, ''ω'' = 0°, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above.

	== Equivalent forms ==		== Equivalent forms ==

Admin: /* Basic format */

2009-01-29T12:58:09Z

Basic format

← Older revision		Revision as of 14:58, 29 January 2009
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	Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.		Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.

	By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, <math>\omega = 180</math>. Optionally, OMEGA angles can be fixed in the ''cis'' position, <math>\omega = 180</math>, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above.		By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, ω = 180° <math>\omega = 180</math>. Optionally, OMEGA angles can be fixed in the ''cis'' position, <math>\omega = 180</math>, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above.

	== Equivalent forms ==		== Equivalent forms ==

Admin: /* Basic format */

2009-01-29T12:57:10Z

Basic format

← Older revision		Revision as of 14:57, 29 January 2009
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	This sequence consists of 14 amino acid residues that are numbered consequtively 11-24.		This sequence consists of 14 amino acid residues that are numbered consequtively 11-24.

	Residue names are case sensitive.		Residue names are case-sensitive.

	Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.		Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.

Admin: /* Non-standard covalent links */

2009-01-29T12:55:33Z

Non-standard covalent links

← Older revision		Revision as of 14:55, 29 January 2009
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	link N 11 C 24		link N 11 C 24

			The purpose of the '''link''' statement is to eliminate the steric repulsion between the two covalently bound atoms and the atoms directly bound to them. The '''link''' statement will ''not'' enforce the formation of a covalent bond between the two atoms. This must be made by explicit distance constraints.

Admin: /* Multiple molecules */

2009-01-29T12:52:12Z

Multiple molecules

← Older revision		Revision as of 14:52, 29 January 2009
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	* '''PL''': Linker from a protein amino acid residue to a linker residue		* '''PL''': Linker from a protein amino acid residue to a linker residue
	* '''LL''': Linker residue		* '''LL''': Linker residue with a virtual bond length of 1 Å
	* '''LL2''': Linker residue		* '''LL2''': Linker residue with a virtual bond length of 2 Å
	* '''LL5''': Linker residue		* '''LL5''': Linker residue with a virtual bond length of 5 Å
	* '''LP''': Linker from a linker residue to a protein amino acid residue		* '''LP''': Linker from a linker residue to a protein amino acid residue

Admin: /* Multiple molecules */

2009-01-29T12:50:57Z

Multiple molecules

← Older revision		Revision as of 14:50, 29 January 2009
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	== Multiple molecules ==		== Multiple molecules ==

			Multiple molecules must be separated by a stretch of "invisible" linker residues:

	GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 1		GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 1
	PL 51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP # linker		PL 51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP # linker
	GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 2		GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 2

			The standard residue library provides the following linker residues:

			* '''PL''': Linker from a protein amino acid residue to a linker residue
			* '''LL''': Linker residue
			* '''LL2''': Linker residue
			* '''LL5''': Linker residue
			* '''LP''': Linker from a linker residue to a protein amino acid residue

	== Non-standard covalent links ==		== Non-standard covalent links ==

Admin: /* Multiple molecules */

2009-01-29T12:47:45Z

Multiple molecules

← Older revision		Revision as of 14:47, 29 January 2009
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	PL 51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP # linker		PL 51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP # linker
	GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 2		GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 2



	== Non-standard covalent links ==		== Non-standard covalent links ==

Admin at 12:47, 29 January 2009

2009-01-29T12:47:28Z

← Older revision		Revision as of 14:47, 29 January 2009
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	GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS		GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS

			== Multiple molecules ==

			GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 1
			PL 51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP # linker
			GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 2



	== Non-standard covalent links ==		== Non-standard covalent links ==

Admin: /* Basic format */

2009-01-29T12:44:57Z

Basic format

← Older revision		Revision as of 14:44, 29 January 2009
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	Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.		Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.

	By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, <math>\omega = 180</math>. Optionally, OMEGA angles can be fixed in the ''cis'' position, <math>\omega = 180</math>, by adding a lower case 'c' in front of the residue name.		By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, <math>\omega = 180</math>. Optionally, OMEGA angles can be fixed in the ''cis'' position, <math>\omega = 180</math>, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above.

	== Equivalent forms ==		== Equivalent forms ==

Admin: /* Basic format */

2009-01-29T12:44:29Z

Basic format

← Older revision		Revision as of 14:44, 29 January 2009
Line 22:		Line 22:
	Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.		Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.

	By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the trans position, <math>\omega = 180</math>.		By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, <math>\omega = 180</math>. Optionally, OMEGA angles can be fixed in the ''cis'' position, <math>\omega = 180</math>, by adding a lower case 'c' in front of the residue name.

	== Equivalent forms ==		== Equivalent forms ==