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+             Installation and Usage Notes for the Validation Application
+                            (Source Distribution)
+
+Note: It is highly recommended to utilize binary distribution,
+since it contains an additional submodule, called PROCHECK, which does more
+structure checking. This source distribution does not contain PROCHECK.
+
+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. It contains subdirectories of various source modules
+    and the following items important for the user:
+
+        bin - subdirectory in which the application executable "validation-v8"
+          will be placed after the build process.
+        data - subdirectory that contains some data files needed by the
+          application. 
+
+
+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
+
+
+2.  Building the Application
+
+a.  Position in the validation-vX.XXX-XXX directory and run "make" command:
+
+        cd validation-vX.XXX-XXX 
+        make
+
+    The application executable "validation-v8" will be placed in the "bin"
+    subdirectory.
+
+
+    NOTE: The users who are working on Sun platform are strongly advised to
+    check the compiler flags in etc/make.platform.sunos5 file. Depending on
+    the compiler version, users may be required to make modifications to those
+    compiler flags.
+
+b.  Make binary data from ASCII data
+
+    - Position in the validation-vX.XXX-XXX directory and run "make" command as
+    follows:
+
+        make binary
+
+    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.
+
+
+3.  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.  <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
+
+NUCHECK:
+Zukang Feng, John Westbrook, Helen M. Berman. NUCheck: Rutgers University,
+New Brunswick, NJ; 1998.  Report No.: NDB-407.
+
+
+