annotate spring_package/pulchra/README @ 17:c790d25086dc draft

"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"

PULCHRA User's Manual
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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