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, 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