Cyana documentation at NYSBC

Reference papers

• http://www.nysbc.net/library/guntert03.pdf

Suggested local procedure

Preparing files

1. Login to the appropriate server, currently %MAINCOMP%

1. 1. make a new directory in form {targetname}CYA
   2. move to the directory
   3. copy one appropriate demo directory and contents from /software/structure/cyana-2.0/demo
      1. auto - automatic use of CANDIDA etc for input from XEASY format - cp /software/structure/cyana-2.0/demo/auto/* .
      2. auto-nmrview - automatic use of CANDIDA etc for input from nmrview - cp /software/structure/cyana-2.0/demo/auto-nmrview/* .
   4. list the files present - ls -l

• .seq files -- simple conversions
  1. from capital to all lower case (for nmrview ) tr '[:upper:]' '[:lower:]' < {yourfile} > {nmrview file}

The authors comments

The mail list contents

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 27 Apr 2005

Nomenclature: The standard residue library of Cyana 2.0 adheres to strict IUPAC nomenclature for amino acids. Compared to the standard libraries of Cyana 1.x and Dyana there are the following changes in atom nomenclature amino acids: Backbone amide proton: HN --> H Glycine alpha protons: HA1/HA2 --> HA2/HA3 The most common forms of the amino acid residues are referred to by the standard three-letter code, i.e. there are the following changes for charged residues: LYS+, ARG+, GLU-, ASP- --> LYS, ARG, GLU, ASP The straightforward way to convert data files to the new nomenclature is by using Cyana itself. The demos include an example script for this purpose, 'MigrateFromDyanaCyana1.cya'. If, for some reason it is desirable to continue using the old Cyana 1.x/Dyana nomenclature together with the new library, this is possible simply by inserting the 'translate dyana' command in the local startup script (./init.cya). The old Cyana 1.x/Dyana library is still available and can be loaded with the 'dyanalib' command, whereas 'cyanalib' will load the standard library that is based on the widely used geometric parameters of Engh and Huber (Acta Crystallogr. A47, 392-400, 1991).

Cyana documentation at NYSBC

Reference papers

Suggested local procedure

Preparing files

The authors comments

The mail list contents

Cyana documentation at NYSBC

Reference papers

• http://www.nysbc.net/library/guntert03.pdf

Suggested local procedure

Preparing files

1. Login to the appropriate server, currently %MAINCOMP%
2. For a new project
   1. make a new directory in form {targetname}CYA
   2. move to the directory
   3. copy one appropriate demo directory and contents from /software/structure/cyana-2.0/demo
      1. auto - automatic use of CANDIDA etc for input from XEASY format - cp /software/structure/cyana-2.0/demo/auto/* .
      2. auto-nmrview - automatic use of CANDIDA etc for input from nmrview - cp /software/structure/cyana-2.0/demo/auto-nmrview/* .
   4. list the files present - ls -l
   5. you need to replace most of the files with those specific to your project. The names of the files are fairly obvious -- aro.* related to aromatics nOes, c13.* to c13 observed non aromatic nOes xpeaks, n15.* related to n15 filtered nOes, demo.seq is the squence file. For using the Cyana data base , see the new nomenclature notes ---

• .seq files -- simple conversions
  1. from capital to all lower case (for nmrview ) tr '[:upper:]' '[:lower:]' < {yourfile} > {nmrview file}

The authors comments

The mail list contents

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 27 Apr 2005

Nomenclature: The standard residue library of Cyana 2.0 adheres to strict IUPAC nomenclature for amino acids. Compared to the standard libraries of Cyana 1.x and Dyana there are the following changes in atom nomenclature amino acids: Backbone amide proton: HN --> H Glycine alpha protons: HA1/HA2 --> HA2/HA3 The most common forms of the amino acid residues are referred to by the standard three-letter code, i.e. there are the following changes for charged residues: LYS+, ARG+, GLU-, ASP- --> LYS, ARG, GLU, ASP The straightforward way to convert data files to the new nomenclature is by using Cyana itself. The demos include an example script for this purpose, 'MigrateFromDyanaCyana1.cya'. If, for some reason it is desirable to continue using the old Cyana 1.x/Dyana nomenclature together with the new library, this is possible simply by inserting the 'translate dyana' command in the local startup script (./init.cya). The old Cyana 1.x/Dyana library is still available and can be loaded with the 'dyanalib' command, whereas 'cyanalib' will load the standard library that is based on the widely used geometric parameters of Engh and Huber (Acta Crystallogr. A47, 392-400, 1991).

Cyana documentation at NYSBC

Suggested local procedure

Preparing files

1. Login to the appropriate server, currently %MAINCOMP%
2. For a new project
   1. make a new directory in form {targetname}CYA
   2. move to the directory
   3. copy one appropriate demo directory and contents from /software/structure/cyana-2.0/demo
      1. auto - automatic use of CANDIDA etc for input from XEASY format - cp /software/structure/cyana-2.0/demo/auto/* .
      2. auto-nmrview - automatic use of CANDIDA etc for input from nmrview - cp /software/structure/cyana-2.0/demo/auto-nmrview/* .
   4. list the files present - ls -l
   5. you need to replace most of the files with those specific to your project. The names of the files are fairly obvious -- aro.* related to aromatics nOes, c13.* to c13 observed non aromatic nOes xpeaks, n15.* related to n15 filtered nOes, demo.seq is the squence file. For using the Cyana data base , see the new nomenclature notes ---

• .seq files -- simple conversions
  1. from capital to all lower case (for nmrview ) tr '[:upper:]' '[:lower:]' < {yourfile} > {nmrview file}

The authors comments

The mail list contents

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 27 Apr 2005

Nomenclature: The standard residue library of Cyana 2.0 adheres to strict IUPAC nomenclature for amino acids. Compared to the standard libraries of Cyana 1.x and Dyana there are the following changes in atom nomenclature amino acids: Backbone amide proton: HN --> H Glycine alpha protons: HA1/HA2 --> HA2/HA3 The most common forms of the amino acid residues are referred to by the standard three-letter code, i.e. there are the following changes for charged residues: LYS+, ARG+, GLU-, ASP- --> LYS, ARG, GLU, ASP The straightforward way to convert data files to the new nomenclature is by using Cyana itself. The demos include an example script for this purpose, 'MigrateFromDyanaCyana1.cya'. If, for some reason it is desirable to continue using the old Cyana 1.x/Dyana nomenclature together with the new library, this is possible simply by inserting the 'translate dyana' command in the local startup script (./init.cya). The old Cyana 1.x/Dyana library is still available and can be loaded with the 'dyanalib' command, whereas 'cyanalib' will load the standard library that is based on the widely used geometric parameters of Engh and Huber (Acta Crystallogr. A47, 392-400, 1991).

Cyana documentation at NYSBC

Suggested local procedure

Preparing files

1. Login to the appropriate server, currently %MAINCOMP%
2. For a new project
   1. make a new directory in form {targetname}CYA

1. 1. 1. auto - automatic use of CANDIDA etc for input from XEASY format - cp /software/structure/cyana-2.0/demo/auto/* .
      2. auto-nmrview - automatic use of CANDIDA etc for input from nmrview - cp /software/structure/cyana-2.0/demo/auto-nmrview/* .
   2. list the files present - ls -l
   3. you need to replace most of the files with those specific to your project. The names of the files are fairly obvious -- aro.* related to aromatics nOes, c13.* to c13 observed non aromatic nOes xpeaks, n15.* related to n15 filtered nOes, demo.seq is the squence file. For using the Cyana data base , see the new nomenclature notes ---

• .seq files -- simple conversions
  1. from capital to all lower case (for nmrview ) tr '[:upper:]' '[:lower:]' < {yourfile} > {nmrview file}

The authors comments

The mail list contents

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 27 Apr 2005

Nomenclature: The standard residue library of Cyana 2.0 adheres to strict IUPAC nomenclature for amino acids. Compared to the standard libraries of Cyana 1.x and Dyana there are the following changes in atom nomenclature amino acids: Backbone amide proton: HN --> H Glycine alpha protons: HA1/HA2 --> HA2/HA3 The most common forms of the amino acid residues are referred to by the standard three-letter code, i.e. there are the following changes for charged residues: LYS+, ARG+, GLU-, ASP- --> LYS, ARG, GLU, ASP The straightforward way to convert data files to the new nomenclature is by using Cyana itself. The demos include an example script for this purpose, 'MigrateFromDyanaCyana1.cya'. If, for some reason it is desirable to continue using the old Cyana 1.x/Dyana nomenclature together with the new library, this is possible simply by inserting the 'translate dyana' command in the local startup script (./init.cya). The old Cyana 1.x/Dyana library is still available and can be loaded with the 'dyanalib' command, whereas 'cyanalib' will load the standard library that is based on the widely used geometric parameters of Engh and Huber (Acta Crystallogr. A47, 392-400, 1991).

Cyana documentation at NYSBC

Suggested local procedure

Preparing files

1. Login to the appropriate server, currently %MAINCOMP%
2. For a new project
   1. make a new directory in form {targetname}CYA
   2. copy an appropriate demo from /software/structure/cyana-2.0/demo
      1. auto - automatic use of CANDIDA etc for input from XEASY format - cp /software/structure/cyana-2.0/demo/auto/* .
      2. auto-nmrview - automatic use of CANDIDA etc for input from nmrview - cp /software/structure/cyana-2.0/demo/auto-nmrview/* .
   3. list the files present - ls -l
   4. you need to replace most of the files with those specific to your project. The names of the files are fairly obvious -- aro.* related to aromatics nOes, c13.* to c13 observed non aromatic nOes xpeaks, n15.* related to n15 filtered nOes, demo.seq is the squence file. For using the Cyana data base , see the new nomenclature notes ---