annotate spring_package/pulchra/README @ 17:c790d25086dc draft

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date Wed, 28 Oct 2020 05:11:56 +0000
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1
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2 PULCHRA User's Manual
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3 ---------------------
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4 PowerfUL CHain Restoration Algorithm
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5 Version 3.04
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6
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7 (c) Piotr Rotkiewicz, 2001-2007, piotr-at-pirx.com
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11 1. Introduction.
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12
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13 PULCHRA is a program for reconstructing full-atom protein models from reduced
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14 representations. PULCHRA can read C-alpha only file and generate an all-atom
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15 output in a very short time. If the initial coordinates are distorted,
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16 PULCHRA will try to optimize the alpha carbon positions to generate
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17 a protein-like structure. Additionally, side chain centers of mass can be used
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18 together with alpha carbons to improve the quality of the reconstruction.
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22 2. Compiling PULCHRA.
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24 PULCHRA comes as a few C source files that can be compiled into a single
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25 executable. No external data files are necessary to run PULCHRA.
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26
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27 To compile PULCHRA with ANSI-C compatible compiler, go to ./src
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28 subdirectory and type:
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30 cc -O3 -o pulchra pulchra.c pulchra_data.c -lm
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32 Because of the static table size, the compilation process can take several seconds.
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35 3. Using PULCHRA.
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37 There are three statically-compiled executables in the PULCHRA archive:
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38 Linux, OS X, and Windows versions, available in ./bin subdirectory.
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39 For security reasons, the Windows executable file is named "pulchra.ex_".
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40 You should rename the file to "pulchra.exe" before running
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41 the program. The executables were statically compiled using GNU C compiler.
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43 PULCHRA can read files in Protein Data Bank format (PDB).
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44
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45 The simplest way of using PULCHRA is:
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47 ./pulchra input.pdb
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49 An output file named "input.rebuilt.pdb" will be created as a result.
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50
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51 To have a better overview of PULCHRA process, a verbose flag (-v) can be used:
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52
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53 ./pulchra -v input.pdb
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54
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55 To display all available options, type:
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56
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57 ./pulchra
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60
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61 4. PULCHRA options.
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62
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63 The following options are recognized by PULCHRA:
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64
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65 -v : enables verbose text output (default: off)
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66
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67 -n : centers input chain coordinates to (0,0,0) (default: off)
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68
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69 -g : use PDB-SG as an input format ("CA" = alpha carbons, "SC" or "CM" = side chain centers of mass)
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70
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71 -c : skips C-alpha positions optimization (default: on)
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72
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73 -p : auto-detects cis-prolins (default: off)
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74
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75 -u value : sets maximum shift from the initial coordinates (default: 0.5A)
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76
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77 -e : rearranges backbone atoms according to AMBER standard (C, O are output after side chain) (default: off)
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78
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79 -b : skips backbone reconstruction (default: on)
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80
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81 -q : optimizes backbone hydrogen bonds pattern, usually gaining a slightly better RMSD, but a little bit more time consuming (default: off)
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82
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83 -s : skips side chains reconstruction (default: on)
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84
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85 -o : doesn't attempt to fix excluded volume conflicts nor punched ring problems (default: on)
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86
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87 -z : doesn't check amino acid chirality (default: on)
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88
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89 -h : outputs hydrogen atoms (default: off)
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90
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91 -r : starts optimization from a random alpha carbon chain rather than from initial coordinates (default: off)
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92
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93 -x : time-seeds random number generator (default: off)
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94
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95 -t : saves chain optimization trajectory to a file <pdb_file.pdb.trajectory>
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96
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97 -i pdbfile : reads the initial C-alpha coordinates from a PDB file
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98
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99
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100
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101 5. PDB format issues.
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102
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103 - PULCHRA will read only first of the multiple occupancy sites (flag ' ' or 'A' in column 17).
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104
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105 - PULCHRA will skip any non-protein residues. Following modified residue codes are
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106 recognized: HID, ASX, GLX, TPO, MSE.
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107
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108
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109
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110 6. Contact and support.
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111
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112 If you encounter issues with PULCHRA, please contact the author: piotr-at-pirx.com
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113