Biowulf High Performance Computing at the NIH
CCP4 on Biowulf

CCP4 (The Collaborative Computational Project Number 4 in Protein Crystallography) is a suite of separate programs which communicate via standard data files, rather than all operations being integrated into one huge program. The programs range from coordinate file manipulations and dataset management to sequence alignment and structure validation.

To use the programs the user must assign input and output files, and run the programs. Often an output file becomes the input to the next step, and system parameter substitution may be used to create filenames in a systematic way. Most crystallographic calculations involve a series of steps in which no decisions need be made until the end, and a command file provides an easy way of chaining calculations.

Standard file formats are defined for the principal data types used in crystallography: reflection data; density maps; and atom coordinates. In defining these formats, a number of trade-offs are made between efficiency (in space and access time), flexibility, portability, and simplicity of use.

There is a policy of continual technical and scientific updates to the suite. Where existing programs have been incorporated into the suite they have often subsequently undergone considerable modification above that needed to use the CCP4 file formats.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

This example aligns 3ESZ onto 3F6R, based on the superposition of the A chains from both PDB entries.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load CCP4
[user@cn3144 ~]$ zcat /pdb/pdb/es/pdb3esz.ent.gz > 3esz.pdb
[user@cn3144 ~]$ zcat /pdb/pdb/f6/pdb3f6r.ent.gz > 3f6r.pdb
[user@cn3144 ~]$ superpose 3esz.pdb -s "A" 3f6r.pdb -s "A" -o 3esz_ON_3f6r.pdb

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

CCP4 also includes an interactive graphical interface. This application requires an X-Windows connection. First source the correct setup file (see above), then type 'ccp4i' at the prompt.

CCP4i window