© Peter Güntert, 2014
Here you can download CYRANGE as a standalone command line tool. Simply select the program version you would like to obtain and click on the Download button.
The file you have downloaded is a zip archive. Save it to disk, then open a terminal window and change to the directory where you saved the file. Once you have done this, enter
unzip 〈archive〉.zip
This command will create a CYRANGE directory in the current working directory. Inside this new directory you will find the CYRANGE command line tool, as well as a README file.
There are no restrictions as to where the CYRANGE executable can be placed; consequently, for the vast majority of users the installation process will be completed after moving the executable to its final location. For further details please consult the README file.
Open a terminal window and enter
[/path/to/cyrange_dir/]cyrange [PARAMETERS] <input_file>
where <input_file> must be in PDB format. The program will calculate the optimum residue ranges for superposition, and output the result on the screen. Each line corresponds to one identified domain. Sample output is shown below:
Optimal range 5..72: RMSD 0.31 A, 0 gaps, 68 residues.
Optimal range 85..104, 118..145: RMSD 0.30 A, 1 gap, 48 residues.
In the above case two separately superimposable domains were found. One of them contains an intra-domain gap of 13 residues. The protein consists of only one polypeptide chain, therefore no chain identifiers are given.
Optimal range A3..A40, A52..A88, B3..B40, B56..B87: RMSD 1.92 A, 3 gaps, 145 residues.
The above CYRANGE output shows that this protein contains just one domain, despite being made up of two chains (A and B).
CYRANGE uses the following parameters:
| Flag | Argument | Symbol* | Description | Default Value |
|---|---|---|---|---|
| -a | real number | δabs | Measure of RMSD decrease required for residue removal. | 1.6 |
| -b | integer | m | Number of residues for padding at domain boundaries. | 3 |
| -d | real number | δ | Measure of RMSD decrease required for residue removal. | 1.2 |
| -g | real number | γ | Penalty factor for gap formation. | 0.4 |
| -gw | integer | - | Minimum size of gaps to be retained in the output. | 3 |
| -h | - | - | Display help and exit. | - |
| -l | file path | - | Customised library file (CYANA format). | built-in library |
| -m | integer | μ | Minimum size for clusters to be considered domains. | 8 |
| -r | range | - | Range of residues to be considered. | all residues |
*as used in the CYRANGE publication.
Providing an input file is compulsory; all other options' default values will be employed unless other values are specified on program invocation.
And finally, here is a long example showing you how to invoke CYRANGE in case you do not want to simply use the parameters' default values:
cyrange -g 0.2 -b 5 -r 20-70,90-130 -l ../my_own.lib my_struct.pdb
This will compute the optimum residue range(s) for my_struct.pdb, using only residues 20 to 70 and 90 to 130. The 'gap' parameter has a value of 0.2 (instead of its default value of 0.4), and 5 instead of 3 residues will be added at each domain boundary before this domain's optimum residue ranges are determined. CYRANGE will employ the user's customised library file '../my_own.lib' instead of the standard library.
PLEASE NOTE: In case your target protein consists of several chains you must specify the residues' chain IDs when giving a range, e.g.
cyrange -r A10-A90 my_struct.pdb