Praktikum Biophysikalische Chemie: Difference between revisions
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* Download the course material: Store the file [[PBCPraktikumCyana.tgz]] in your home directory. | * Download the course material: Store the file [[PBCPraktikumCyana.tgz]] in your home directory. | ||
* Unpack the data: | * Unpack the data: | ||
tar zxf PBCPraktikumCyana.tgz | tar zxf PBCPraktikumCyana.tgz | ||
* Run the setup command: | * Run the setup command: | ||
setup_cyana | setup_cyana | ||
* Make a new directory for the structure calculation, and change into it: | * Make a new directory for the structure calculation, and change into it: | ||
| Line 13: | Line 16: | ||
mkdir vaso | mkdir vaso | ||
cd vaso | cd vaso | ||
* Use a text editor to write a new file, '''vaso.seq''', that contains the peptide sequence, one upper-case residue name per line, given in the standard three-letter code for amino acids (except for cysteine residues that are involved in a disulfide bond, which are denoted by "CYSS"), e.g. | * Use a text editor to write a new file, '''vaso.seq''', that contains the peptide sequence, one upper-case residue name per line, given in the standard three-letter code for amino acids (except for cysteine residues that are involved in a disulfide bond, which are denoted by "CYSS"), e.g. | ||
| Line 25: | Line 29: | ||
ARG | ARG | ||
GLY | GLY | ||
* Use a text editor to write a new initialization script, '''init.cya''', for the program CYANA with the following content: | * Use a text editor to write a new initialization script, '''init.cya''', for the program CYANA with the following content: | ||
| Line 32: | Line 37: | ||
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. | ||
* Use a text editor to write a new file, vaso.upl, that contains the upper distance bounds derived from NOESY cross peaks, using the following format: | * Use a text editor to write a new file, vaso.upl, that contains the upper distance bounds derived from NOESY cross peaks, using the following format: | ||
Revision as of 17:40, 9 January 2009
- Download the course material: Store the file PBCPraktikumCyana.tgz in your home directory.
- Unpack the data:
tar zxf PBCPraktikumCyana.tgz
- Run the setup command:
setup_cyana
- Make a new directory for the structure calculation, and change into it:
mkdir vaso cd vaso
- Use a text editor to write a new file, vaso.seq, that contains the peptide sequence, one upper-case residue name per line, given in the standard three-letter code for amino acids (except for cysteine residues that are involved in a disulfide bond, which are denoted by "CYSS"), e.g.
CYSS TYR PHE GLN ASN CYSS PRO ARG GLY
- Use a text editor to write a new initialization script, init.cya, for the program CYANA with the following content:
cyanalib read seq vaso.seq
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.
- Use a text editor to write a new file, vaso.upl, that contains the upper distance bounds derived from NOESY cross peaks, using the following format:
91 THR HB 93 GLN QB 5.50 80 SER HB2 81 ILE H 4.22 80 SER HB3 81 ILE H 4.22 81 ILE HA 84 LEU H 4.01 81 ILE HA 84 LEU HB2 4.47 81 ILE HA 81 ILE QG2 3.46 81 ILE HA 81 ILE HG12 3.77 28 VAL HA 39 LEU HG 3.97 52 SER H 52 SER HB2 3.96 52 SER H 52 SER HB3 3.96 99 SER QB 101 VAL H 5.50 43 SER H 43 SER QB 3.12 43 SER QB 48 GLU H 4.07 42 GLU HA 43 SER QB 5.50 43 SER QB 48 GLU HB2 3.95