Installation and Usage Notes for the CifTr Application (Binary Distribution) 1. Installation a. Uncompress and unbundle the distribution using the following command: zcat ciftr-vX.X-XXX.tar.gz | tar -xf - The result of this command is a subdirectory ciftr-vX.X-XXX in the current directory, which has several items: bin - subdirectory that contains the application executable "CifTr" data - subdirectory that contains some data files needed by the application. etc - subdirectory that contains utility scripts and application software license agreement. testdata - subdirectory that contains the sample input files to the application. testresult - subdirectory that contains the output files after the application has been run on the sample input files. test.sh - the test script used to demonstrate the application. It uses the files from "testdata" subdirectory as its input and stores its output to the files in "testresult" directory. b. Set up the environment variables. - Define RCSBROOT environment variable to point to the installation directory. Assuming that the installation directory is /home/username/ciftr-vX.X-XXX, execute in the shell: For C shell users: setenv RCSBROOT /home/username/ciftr-vX.X-XXX For Bourne shell users: RCSBROOT=/home/username/ciftr-vX.X-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 ciftr-vX.X-XXX/etc directory and run the script binary.sh: cd ciftr-vX.X-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. Demonstration a. Position in the ciftr-vX.X-XXX directory and run the test.sh script: cd ciftr-vX.X-XXX ./test.sh The script takes the names of all files in "testdata" subdirectory and stores them in a separate file, which is used as in input to the "CifTr" application. The resulting output files are stored in "testresult" subdirectory. 3. Application Usage Notes Usage CIFTr [-i filename] [-f filelist] [-NO_CHAIN_ID] [-IUPAC_H_ATOMS] [-output_path pathname] [-extension file_extension] [-uncompress uncompress_command] [-compress compress_command] CIFTr can translate single or multiple files in mmCIF format into files in PDB format. CIFTr provides the option of producing a file with an empty chain ID field for structures with a single chain, and the option of producing files with standard IUPAC hydrogen nomenclature for standard L-amino acids. Options for file location, naming, and compression are also provided. For Single Files To translate a single file in mmCIF format to PDB format, at the UNIX prompt type: CIFTr -i filename The output file will have the same name as the input file with the extension .pdb (i.e., filename.pdb). For Multiple Files To translate several files in mmCIF format to PDB format, create a file that contains the names of all of the files that need to be translated. The file (in this example, named filelist) should resemble: first_file_name second_file_name third_file_name At the UNIX prompt, type: CIFTr -f filelist to translate the files in mmCIF format to files in PDB format. Chain ID CIFTr -i filename -NO_CHAIN_ID CIFTr -f filelist -NO_CHAIN_ID CIFTr can create PDB file(s) with an empty chain ID field if the file has only one chain. The program default is to include a chain ID. IUPAC Hydrogen Nomenclature CIFTr -i filename -IUPAC_H_ATOMS CIFTr -f filelist -IUPAC_H_ATOMS CIFTr can create PDB file(s) with standard IUPAC hydrogen nomenclature for standard L-amino acids. The default is to use conventional PDB nomenclature. Although the IUPAC option changes the H-atom numbering according to follow IUPAC conventions, the organization and spacing within the atom name field continues to follow PDB rules. This permits software applications to reliably locate the element symbol within the atom name. Other options: file location, naming, and compression CIFTr -i filename -output_path pathname CIFTr -f filelist -output_path pathname Option -output_path is used to specified the output directory. The default is the current directory. CIFTr -i filename -extension file_extension CIFTr -f filelist -extension file_extension Option -extension specifies the extension given to the generated PDB format file. The default is the input file name with the extension '.pdb'. For example, if the name of the mmCIF file is 1A00.cif, after translation, the default pdb file name will be 1A00.cif.pdb. The option -extension pdb, for example, would name the file 1A00.pdb. CIFTr -i filename -uncompress uncompress_command CIFTr -f filelist -uncompress uncompress_command Option -uncompress should be used if the input files are compressed. The program uses the system call 'uncompress_command' to uncompress files and assumes the 'uncompress_command' exists in the current environment. CIFTr uses the 'uncompress_command' as 'uncompress_command < input_file'. For example, CIFTr -i 1a00.cif.gz -uncompress gunzip would translate the uncompressed CIF format file 1a00.cif into 1a00.cif.pdb CIFTr -i filename -compress compress_command CIFTr -f filelist -compress compress_command Option -compress is used to compress the files created by the program. CIFTr uses the system call 'compress_command' to compress files and assumes the 'compress_command' exists in the current environment. CIFTr uses the 'compress_command' as 'compress_command -f output_file'. For example, CIFTr -i 1a00.cif -compress gzip would create a PDB format file compressed by the program gzip -- 1a00.cif.pdb.gz