Strukturrechnung mit CYANA (2015)
(→Startup) |
(→Startup) |
||
| Line 17: | Line 17: | ||
cd guentert | cd guentert | ||
| − | The | + | The programm shows the list of the files in the active directory on the left side. This enables you to open them within windows by clicking them and in addition this allows you to copy files into and from the directory by drag and drop. |
Revision as of 12:33, 14 January 2015
Contents |
Startup
Log in to the Windows system with the username and password of your HRZ account.
The structure calculation will be performed on a Linux server that can be accessed by a remote connection to our computer cluster. For the remote connection we use the program MobaXterm. This program provides a shell eviroment in Windows that allows us the access to the remote computer. To etablish the connection to our server please follow the fowlling steps:
- Copy the ZIP file in T:/Struktrurechnung/MobaXterm@honshu.zip to you personal folder U: and unpack it.
- The folder contains two files MobaXterm_Personal_7.4.exe (the program executable and an adittional file containing all passwords and data necessary to automaticall access the server
- Start the program by klicking the execuatble
- The program starts with a default shell console (balck area). Additionally you see on the left side a field named "Saved session". There, please click on the preconfigured connection 141.2.222.9 to connect. An new tab should open showing the prompt "honsh>". This is the name of our server.
All students use the same account so as an first step please create a directory for your group to work in. For that the folling steps are necessary:
- use the command 'mkdir' command to create a directory. Please chose the last name of one of the members (use only letters and no explicit german letters). (Every group name has to be uniqe) E.g. if we want to use 'geuntert' as the groupname we type
mkdir guentert
- now change the directory using the command 'cd'. So for our example:
cd guentert
The programm shows the list of the files in the active directory on the left side. This enables you to open them within windows by clicking them and in addition this allows you to copy files into and from the directory by drag and drop.
clicking the icon labeled BCC Linux Terminal-Service.nxs. The username and password for the Linux server are the same as for the Windows XP computer, and the data in the home directories are shared between the two systems.
Download the data for the practical: Data.tgz and store it in your home directory.
In a terminal window, unpack the data and start the bash shell
tar zxf Data.tgz bash
Three subdirectories will be created:
- cyana1: structure calculation using only the assigned 15N-resolved NOESY peak list
- cyana2: structure calculation using the assigned 15N-resolved NOESY peak list and the unassigned 13C-resolved NOESY peak list
- cyana3: structure calculation using the unassigned 15N-resolved and 13C-resolved NOESY peak lists
Enter the corresponding subdirectory. For example
cd cyana1
and copy your data to this directory. For example, for the 'cyana1' calculation, copy your chemical shift list (shifts.prot) and your assigned peak list from the 15N-resolved NOESY spectrum (n15assigned.peaks).
Run the CYANA structure calculation
Start CYANA, and execute the CYANA script CALC.cya (in 'cyana1') or AUTO.cya (in 'cyana2' and 'cyana3'):
> cyana
___________________________________________________________________
CYANA 3.0 (intel)
Copyright (c) 2002-10 Peter Guntert. All rights reserved.
___________________________________________________________________
Library file "/usr/local/soft/cyana-3.0/lib/cyana.lib" read, 38 residue types.
Sequence file "sequence.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, cyana.ovw ('cyana1') or final.ovw ('cyana2' and 'cyana3'), and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, cyana.pdb ('cyana1') or final.pdb ('cyana2' and 'cyana3').
The overview file has at least three parts. The file starts with a table of the target function values and restraint violation statistics. For example:
Structural statistics:
str target upper limits van der Waals torsion angles
function # rms max # sum max # rms max
1 1.69 2 0.0076 0.36 4 5.6 0.34 0 0.3302 3.23
2 1.74 2 0.0077 0.36 5 5.9 0.34 0 0.3272 3.30
3 1.75 1 0.0075 0.36 5 5.7 0.34 0 0.3695 3.45
4 1.87 1 0.0075 0.37 7 6.3 0.34 0 0.3159 2.69
5 1.95 1 0.0075 0.37 5 6.7 0.37 0 0.3185 3.00
6 2.12 2 0.0084 0.36 6 6.6 0.34 0 0.3745 3.56
7 2.19 2 0.0100 0.50 7 6.8 0.34 0 0.3257 3.29
8 2.35 2 0.0096 0.36 8 7.0 0.34 0 0.3748 3.50
9 2.40 2 0.0088 0.36 5 8.4 0.35 0 0.4152 3.44
10 2.49 2 0.0090 0.36 9 7.6 0.33 0 0.3494 3.20
Ave 2.06 2 0.0084 0.38 6 6.7 0.34 0 0.3501 3.26
+/- 0.28 0 0.0009 0.04 2 0.8 0.01 0 0.0308 0.25
Min 1.69 1 0.0075 0.36 4 5.6 0.33 0 0.3159 2.69
Max 2.49 2 0.0100 0.50 9 8.4 0.37 0 0.4152 3.56
Cut 0.20 0.20 5.00
This table has one row for each structure, containing
- the rank of the structure sorted by target function value
- the target function value
- three columns for each type of conformational restraints:
- the number of restraints that are violated by more than the cutoff value given in the last row (“Cut”)
- the root-mean-square (RMS) violation calculated over all, violated and fulfilled, restraints of this type
- the maximal violation
The five bottom lines of the Table give the average value, the standard deviation, the minimum value, and the maximum value of the corresponding quantity over the individual structures, as well as the cutoff value for significant violations.
Restraints that are violated in a significant number of structures by more than the corresponding cutoff value are reported in the second part of the overview file:
Constraints violated in 3 or more structures:
# mean max. 1 5 10
Upper QB LEU 17 - QB PRO 108 3.69 3 0.10 0.50 ++ * peak 1009
Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.37 +++*++++++ peak 803
VdW N ILE 81 - HD2 PRO 82 2.45 10 0.34 0.37 ++++*+++++
VdW CG2 ILE 81 - C ILE 81 2.90 6 0.20 0.21 + + ++* +
2 violated distance restraints.
0 violated angle restraints.
Each line identifies a violated restraint, and gives the number of structures in which the restraint is violated by more than the aforementioned cutoff value (column labeled “#”), its maximal violation (column “max.”), and the structures in which the violations occur (a one-character column for each structure that is analyzed). Structures in which the restraint is violated by more than the cutoff are marked with “+”, or with a “*” for the structure in which the maximal violation occurs. If available, the number of the cross peak from which the restraint originated is given at the end of the line.
At the end of the overview file, root-mean-square deviation (RMSD) values for the atom positions after optimal superposition of the individual conformers onto the mean coordinates are given:
RMSDs for residues 10..100: Average backbone RMSD to mean : 0.58 +/- 0.11 A (0.45..0.82 A; 10 structures) Average heavy atom RMSD to mean : 1.08 +/- 0.11 A (0.93..1.25 A; 10 structures)
The residue range used for the superposition is indicated. RMSD values are computed for the backbone and heavy atoms of the given residues. The average value, the standard deviation, and the minimal and maximal values of the RMSDs between the analyzed structures and their mean coordinates are calculated.
Visualize the structure
The program MOLMOL can visualize the bundle of conformers that represents the solution structure of the peptide with the command
molmol -r 7-37 cyana.pdb
to start the program MOLMOL and to show a superposition of the 10 conformers whose coordinates are stored in the PDB file cyana.pdb. The option "-r 7-37" indicates MOLMOL to optimally superimpose the backbone atoms of residues 8-21.
Alternatively, other molecular viewers such as 'pymol' can be used.
