Access to CHI is provided by:

% source chi-directory/chi_env

this should be sourced from a .cshrc file.

Once you have sourced the setup file (see above) a variety of commands will now be available to perform helix searching. All these commands begin with the prefix chi_ to distinguish them from any other commands. The commands are:

• chi_create - create the starting structure
• chi_search - perform search
• chi_rmsd - compute RSMDs between structures
• chi_cluster - find clusters of structures
• chi_average - average coordinates in clusters
• chi_expand - expand clusters to higher-order oligomers
• chi_spread - calculate spread of structures in clusters
• chi_interaction - calculate per-residue interaction energies
• chi_plot - create Xmgr plot files
• chi_help - startup the HTML documentation
• chi_edit - edit chi_param file

Files needed to run a search:

The CHI package must have a description of the molecule (its primary sequence), and the parameters of the search. This information is all contained in the file chi_param:

chi_param

This file contains information which define the molecule, the sequence of the helices and the parameters of the search. These parameters are broken up into sections with headings. The parameters are all annotated (by comments in curly braces - {}). Things which should be considered for changing by the user are preceeded by a {===>}:

{* name of the molecule *}

{===>} evaluate ($mol="GpA")

{* number of helices *}

{===>} evaluate ($nhelices=2)




There are web-based tools available for creating and editing a chi_param file. The HTML-based editor can be started from the Unix command line using the chi_edit command (eg. chi_edit chi_param.

Where to run a search

Users should create a unique directory for each molecule and sequence to be studied - the name of the directory is not important. The chi_param file (described above) should be located in this directory. The CHI commands are run in this directory. A subdirectory will be created called results - this will contain the results of the chi programs:

for example: user paul makes a directory called GpA for glycophorin searches. In this directory he places the appropriate chi_param file. After running the first CHI program (chi_create) the directory now contains a subdirectory called results. The directory also contains the starting molecular structure file and coordinates (GpA.psf and GpA.pdb).

Running the search

The programs should generally be run in the following order (although some programs may not be needed depending on the particular molecule). An indication of the computing required for each program is given below.

create initial structure (fast)

chi_create

output: results/create.out

run the search (slow)

chi_search or chi_search -nproc number

output: results/search.out and results/[left,right]_*.pdb

calculate RMSDs between structures (slow)

chi_rmsd or chi_rmsd -nproc number

output: results/rmsd.out

calculate clusters (very fast)

chi_cluster

output: results/cluster.out

calculate average structures from clusters (medium)

chi_average

output: results/average.out and results/cluster*.pdb

calculate spread of structures in a cluster around the average (fast)

chi_spread

output: results/spread.out

expand a homodimer to the nearest higher order oligomer (medium)

chi_expand

output: results/expand.out and results/cluster_*.pdb

calculate interaction energy between residues (fast)

chi_interaction

output: results/interaction.out

plot results (fast)

chi_plot

output: results/*.xmgr

Possible problems

• In the event that CNS/PCNS is not installed on the current machine no error message will be given when the file chi_env is sourced, but when the chi programs are executed they will terminate.
• There may be bugs present in the input files. In order to obtain a copy of the output of the programs they can be run with the option -verbose. This will create a file called <program name>.log - for example, chi_average.log. However, note that for some programs (chi_search in particular), the output files are large (several megabytes).