Installation and Usage Notes for the Validation Application
(Binary Distribution)
Note: The binary distribution contains an additional submodule, called PROCHECK,
which does more structure checking. This submodule is not available in the
source distribution.
1. Installation
a. Uncompress and unbundle the distribution using the following command:
zcat validation-vX.XXX-XXX.tar.gz | tar -xf -
The result of this command is a subdirectory validation-vX.XXX-XXX in the
current directory, which contains the following:
bin - subdirectory that contains application executable "validation-v8"
data - subdirectory that contains some data files needed by the
application.
etc - subdirectory that contains utility scripts and application
software license agreement.
procheck - subdirectory that contains executables for "procheck"
b. Set up the environment variables.
- Define the RCSBROOT environment variable to point to the installation
directory. Note that the RCSBROOT environment is also used for other RCSB
applications like ADIT and PDB_EXTRACT. If all these applications are
running on a computer, the last instance of setenv command will define the
environment. Thus, set the environment at the command line as follows,
just prior to running the application. Assuming that the installation
directory is
/home/username/validation-vX.XXX-XXX, execute in the shell:
For C shell users:
setenv RCSBROOT /home/username/validation-vX.XXX-XXX
For Bourne shell users:
RCSBROOT=/home/username/validation-vX.XXX-XXX; export RCSBROOT
- Add "bin" subdirectory to the PATH environment variable.
Execute in the shell:
For C shell users:
setenv PATH "$RCSBROOT/bin:"$PATH
For Bourne shell users:
PATH="$RCSBROOT/bin:"$PATH; export PATH
c. Make binary data from ASCII data
- Position in the validation-vX.XXX-XXX/etc directory and run the script
binary.sh:
cd validation-vX.XXX-XXX/etc
./binary.sh
This command will create certain binary data files, using the ASCII data
files in data/ascii directory. The resulting files are stored in
data/binary directory. Note that it may take several minutes for this
step to complete. This step must be executed before the tool can be
utilized.
2. Application Usage Notes
Usage:
For mmCIF files (Please note, only mmCIF format files downloaded from the PDB
or generated by PDB_EXTRACT should be used):
validation-v8 -f file_name -o 2 -adit -exchange -public
For PDB files:
validation-v8 -f file_name -o 0 -adit
For example, to create reports for a file in mmCIF format named 1xyz.cif
type:
validation-v8 -f 1xyz.cif -o 2 -adit -exchange -public
Output:
The names of the output files begin with the root identifier <ID>,
which is followed by an extension that indicates the file type.
For a PDB format file, the program converts the file name without
extension into uppercase for the <ID>. For an mmCIF format file, the program
uses data block identifier as the <ID>.
The application creates the following files:
A. <ID>.letter: a text file that contains a summary validation letter.
B. <ID>.ps: a PostScript file that contains molecular graphics of the structure.
For crystal structures, this includes a view of the asymmetric unit
and crystal packing. If the mmCIF file was validated and the biological unit
of the entry is either larger or smaller than the asymmetric unit, and the
struct_biol_gen category was appropriately completed in the mmCIF
file, then a view of the biological unit(s) will be included.
For NMR ensemble structures, a view of the first model and the ensemble
of all models is included. If the NMR entry contains one model, a view
of the model will be included.
NUCHECK output: If the structure contains nucleic acids, the <ID>.ps file also
includes plots describing the geometry, torsion, and base morphology of the
nucleic acids generated by the program NUCHECK.
C. PROCHECK output: For crystal structures containing protein, there are ten
PostScript files from PROCHECK:
File name / File contains
<ID>_01.ps: Ramachandran plot
<ID>_02.ps: Ramachandran plots by residue
<ID>_03.ps: Chi1-Chi2 plots
<ID>_04.ps: Main-chain parameters
<ID>_05.ps: Side-chain parameters
<ID>_06.ps: Residue properties
<ID>_07.ps: Main-chain bond distance comparisons
<ID>_08.ps: Main-chain bond angle comparisons
<ID>_09.ps: RMS deviations from planarity
<ID>_10.ps: Summary of geometrical distortions
For NMR structures containing protein, there are nine PostScript files from
PROCHECK:
File name / File contains
<ID>_01.ps: Ramachandran plot
<ID>_02.ps: Ramachandran plots for all residue types
<ID>_03.ps: Chi1-Chi2 plots
<ID>_04.ps: Chi1 frequency distributions
<ID>_05.ps: Chi2 frequency distributions
<ID>_06.ps: Ensemble Ramachandran plots
<ID>_07.ps: Residue properties
<ID>_08.ps: Equivalent resolution
<ID>_09.ps: Model secondary structures
D. <ID>.html: This html file is an Atlas summary containing the following:
For all structures:
The sequence of the residues in each chain (from entity_poly for a mmCIF file,
from SEQRES for a PDB file, or from the coordinates if entity_poly or SEQRES
are not provided).
Citation information (if provided).
Refinement information (if provided).
For crystal structures, additional information is listed:
Space group and cell constants.
Crystallization conditions (if provided).
Refinement information (if provided).
3. REFERENCES
PROCHECK:
Roman A. Laskowski, Malcolm W. MacArthur, David S. Moss and Janet M. Thornton
(1993).
PROCHECK: a program to check the stereochemical quality of protein structures.
J. Appl. Cryst., 26, 283-291.
A. Louise Morris, Malcolm W. MacArthur, E. Gail Hutchinson and
Janet M. Thornton (1992).
Stereochemical quality of protein structure coordinates.
Proteins, 12, 345-364.
NUCHECK:
Zukang Feng, John Westbrook, Helen M. Berman. NUCheck: Rutgers University,
New Brunswick, NJ; 1998. Report No.: NDB-407.