Praktikum Biophysikalische Chemie: Difference between revisions
| Line 75: | Line 75: | ||
read upl vaso.upl | read upl vaso.upl | ||
ssbond 1- | ssbond 1-6 | ||
calc_all 50 steps=3000 | calc_all 50 steps=3000 | ||
overview vaso.ovw structures=10 pdb | overview vaso.ovw structures=10 pdb | ||
The '''read upl''' command reads the input file with upper distance limits, vaso.upl. The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used. The '''overview''' command sorts the resulting structures by ascending target function value, analyzes the 10 best conformers for violations of the conformational restraints, and saves the results of the analysis in an overview file, '''vaso.ovw''', and the coordinates of the 10 best conformers in a PDB file, '''vaso.pdb'''. | The '''read upl''' command reads the input file with upper distance limits, vaso.upl. | ||
The '''ssbond''' command adds restraints for the disulfide bond between residues Cys1 and Cys6. | |||
The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used. | |||
The '''overview''' command sorts the resulting structures by ascending target function value, analyzes the 10 best conformers for violations of the conformational restraints, and saves the results of the analysis in an overview file, '''vaso.ovw''', and the coordinates of the 10 best conformers in a PDB file, '''vaso.pdb'''. | |||
=== Run the CYANA structure calculation === | === Run the CYANA structure calculation === | ||
Revision as of 22:47, 9 January 2009
Download and install the course material
Store the file PBCPraktikumCyana.tgz in your home directory and execute the setup command:
tar zxf PBCPraktikumCyana.tgz setup_cyana
Make a new directory for the structure calculation, and change into it:
mkdir vaso cd vaso
Write the sequence file
Use a text editor to write a new file called 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
Write the initialization script
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.
Write the NOE distance restraint file
Use a text editor to write a new file, vaso.upl, that contains the upper distance bounds derived from NOESY cross peaks, using the standard CYANA nomenclature for atoms in proteins and the same format as in the following example:
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
Each line specifies an upper bound on the distance between two hydrogen atoms. The data in the 7 columns are:
- First residue number
- First residue name
- First atom name
- Second residue number
- Second residue name
- Second atom name
- Upper distance bound in Å
Residue and atom names are given in upper case letters. The exact number of spaces between different items is irrelevant, but the "TAB" key should not be used.
Note that the backbone amide hydrogen is called "H", not "HN".
Degenerate groups of atoms, e.g. methyl groups, and diastereotopic pairs of hydrogen atoms, e.g. HB2/HB3 in serine, are referred to by "pseudoatoms" whose names are derived from the names of the hydrogen atoms that they represent by changing the first letter from "H" to "Q" and omitting the last digit. For instance, "HB2" and "HB3" are represented by a pseudoatom called "QB".
Write the CYANA script to execute the structure calculation
Use a text editor to write a new CYANA script, CALC.cya, with the following content:
read upl vaso.upl ssbond 1-6 calc_all 50 steps=3000 overview vaso.ovw structures=10 pdb
The read upl command reads the input file with upper distance limits, vaso.upl.
The ssbond command adds restraints for the disulfide bond between residues Cys1 and Cys6.
The calc_all command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used.
The overview command sorts the resulting structures by ascending target function value, analyzes the 10 best conformers for violations of the conformational restraints, and saves the results of the analysis in an overview file, vaso.ovw, and the coordinates of the 10 best conformers in a PDB file, vaso.pdb.
Run the CYANA structure calculation
Start CYANA, and execute the CYANA script CALC.cya:
> cyana
___________________________________________________________________
CYANA 3.0 (intel)
Copyright (c) 2002-08 Peter Guntert. All rights reserved.
___________________________________________________________________
Library file "/usr/local/soft/cyana-3.0/lib/cyana.lib" read, 38 residue types.
Sequence file "demo.seq" read, 114 residues.
cyana> CALC
Analyze the results of the structure calculation
The results of the structure calculation are the structural statistics in the overview file, vaso.ovw, and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, vaso.pdb.