Praktikum Biophysikalische Chemie

• 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: