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-
-PULCHRA User's Manual
----------------------
-PowerfUL CHain Restoration Algorithm
-Version 3.04
-
-(c) Piotr Rotkiewicz, 2001-2007, piotr-at-pirx.com
-
-
-
-1. Introduction.
-
-PULCHRA is a program for reconstructing full-atom protein models from reduced
-representations. PULCHRA can read C-alpha only file and generate an all-atom
-output in a very short time. If the initial coordinates are distorted,
-PULCHRA will try to optimize the alpha carbon positions to generate
-a protein-like structure. Additionally, side chain centers of mass can be used
-together with alpha carbons to improve the quality of the reconstruction.
-
-
-
-2. Compiling PULCHRA.
-
-PULCHRA comes as a few C source files that can be compiled into a single
-executable. No external data files are necessary to run PULCHRA.
-
-To compile PULCHRA with ANSI-C compatible compiler, go to ./src
-subdirectory and type:
-
-cc -O3 -o pulchra pulchra.c pulchra_data.c -lm
-
-Because of the static table size, the compilation process can take several seconds.
-
-
-3. Using PULCHRA.
-
-There are three statically-compiled executables in the PULCHRA archive:
-Linux, OS X, and Windows versions, available in ./bin subdirectory.
-For security reasons, the Windows executable file is named "pulchra.ex_".
-You should rename the file to "pulchra.exe" before running
-the program. The executables were statically compiled using GNU C compiler.
-
-PULCHRA can read files in Protein Data Bank format (PDB).
-
-The simplest way of using PULCHRA is:
-
-./pulchra input.pdb
-
-An output file named "input.rebuilt.pdb" will be created as a result.
-
-To have a better overview of PULCHRA process, a verbose flag (-v) can be used:
-
-./pulchra -v input.pdb
-
-To display all available options, type:
-
-./pulchra
-
-
-
-4. PULCHRA options.
-
-The following options are recognized by PULCHRA:
-
-  -v : enables verbose text output (default: off)
-
-  -n : centers input chain coordinates to (0,0,0) (default: off)
-
-  -g : use PDB-SG as an input format ("CA" = alpha carbons, "SC" or "CM"  = side chain centers of mass)
-
-  -c : skips C-alpha positions optimization (default: on)
-
-  -p : auto-detects cis-prolins (default: off)
-
-  -u value : sets maximum shift from the initial coordinates (default: 0.5A)
-
-  -e : rearranges backbone atoms according to AMBER standard (C, O are output after side chain) (default: off)
-
-  -b : skips backbone reconstruction (default: on)
-
-  -q : optimizes backbone hydrogen bonds pattern, usually gaining a slightly better RMSD, but a little bit more time consuming (default: off)
-
-  -s : skips side chains reconstruction (default: on)
-
-  -o : doesn't attempt to fix excluded volume conflicts nor punched ring problems (default: on)
-
-  -z : doesn't check amino acid chirality (default: on)
-
-  -h : outputs hydrogen atoms (default: off)
-
-  -r : starts optimization from a random alpha carbon chain rather than from initial coordinates (default: off)
-
-  -x : time-seeds random number generator (default: off)
-
-  -t : saves chain optimization trajectory to a file <pdb_file.pdb.trajectory>
-
-  -i pdbfile : reads the initial C-alpha coordinates from a PDB file
-
-
-
-5. PDB format issues.
-
-- PULCHRA will read only first of the multiple occupancy sites (flag ' ' or 'A' in column 17).
-
-- PULCHRA will skip any non-protein residues. Following modified residue codes are
-recognized: HID, ASX, GLX, TPO, MSE.
-
-
-
-6. Contact and support.
-
-If you encounter issues with PULCHRA, please contact the author: piotr-at-pirx.com
-