Standardize your PDB files¶
rna_standardize.py¶
rna_standardize.py - standardzie RNA PDB structures
Usage:
$ rna_standardize.py
-v is for verbose, –version for version ;)
usage: rna_standardize.py [-h] [--version] [--no-progress-bar] [--renum-nmr]
[--inplace] [-v] [--dont-replace-hetatm]
[--keep-hetatm] [--here] [--no-hr]
[--dont-fix-missing-atoms] [--mdr]
[--renumber-residues] [--suffix SUFFIX]
[--dont-report-missing-atoms] [--dont-rename-chains]
[--backbone-only] [--no-backbone] [--bases-only]
file [file ...]
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file¶ file
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-h,--help¶ show this help message and exit
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--version¶
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--no-progress-bar¶ for –no-progress-bar for –rpr
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--renum-nmr¶
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--inplace¶ in place edit the file! [experimental, only for get_rnapuzzle_ready, –delete, –get-ss, –get-seq, –edit-pdb]
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-v,--verbose¶ tell me more what you’re doing, please!
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--dont-replace-hetatm¶ replace ‘HETATM’ with ‘ATOM’ [tested only with –get-rnapuzzle-ready]
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--keep-hetatm¶ keep hetatoms, [if not replaced anyway with ATOM, see –dont-replace-hetatm
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--here¶ save a file next to the original file with auto suffix for –extract it’s .extr.pdb
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--no-hr¶ do not insert the header into files
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--dont-fix-missing-atoms¶ used only with –get-rnapuzzle-ready
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--mdr¶ get structures ready for MD (like rpr but without first)
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--renumber-residues¶ by defult is false
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--suffix<suffix>¶ when used with –inplace allows you to change a name of a new file, –suffix del will give <file>_del.pdb (mind added _)
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--dont-report-missing-atoms¶ used only with –get-rnapuzzle-ready
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--dont-rename-chains¶ used only with –get-rnapuzzle-ready. By default: –get-rnapuzzle-ready rename chains from ABC.. to stop behavior switch on this option
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--backbone-only¶ used only with –get-rnapuzzle-ready, keep only backbone (= remove bases)
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--no-backbone¶ used only with –get-rnapuzzle-ready, remove atoms of backbone (define as P OP1 OP2 O5’)
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--bases-only¶ used only with –get-rnapuzzle-ready, keep only atoms of bases
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class
rna_tools.rna_tools_lib.RNAStructure(fn)[source]¶ RNAStructure - handles an RNA pdb file.
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fn¶ path to the structural file, e.g., “../rna_tools/input/4ts2.pdb”
Type: string
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name¶ filename of the structural file, “4ts2.pdb”
Type: string
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get_rnapuzzle_ready(renumber_residues=True, fix_missing_atoms=True, rename_chains=True, ignore_op3=False, report_missing_atoms=True, keep_hetatm=False, backbone_only=False, no_backbone=False, bases_only=False, save_single_res=False, verbose=False)[source]¶ Get rnapuzzle (SimRNA) ready structure.
Clean up a structure, get current order of atoms.
Parameters: - renumber_residues – boolean, from 1 to …, second chain starts from 1 etc.
- fix_missing_atoms – boolean, superimpose motifs from the minilibrary and copy-paste missing atoms, this is super crude, so should be used with caution.
Submission format @http://ahsoka.u-strasbg.fr/rnapuzzles/
Run
rna_tools.rna_tools.lib.RNAStructure.std_resn()before this function to fix names.
Figure: (Starting from left) input structure, structure with rebuilded atoms, and reference. The B fragment is observed in the reference used here as a “benchmark”, fragment A is reconstructed atoms (not observed in the reference”). 201122
- 170305 Merged with get_simrna_ready and fixing OP3 terminal added
- 170308 Fix missing atoms for bases, and O2’
Fig. Add missing O2’ atom (before and after).
Fig. The residue to fix is in cyan. The G base from the library in red. Atoms O4’, C2’, C1’ are shared between the sugar (in cyan) and the G base from the library (in red). These atoms are used to superimpose the G base on the sugar, and then all atoms from the base are copied to the residues.
Fig. Rebuild ACGU base-less. It’s not perfect but good enough for some applications.
Warning
It was only tested with the whole base missing!
Warning
requires: Biopython
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Atoms order¶
Atoms order, A as an example:
ATOM 1 P G A 1 50.626 49.730 50.573 1.00100.19 P
ATOM 2 OP1 G A 1 49.854 48.893 49.562 1.00100.19 O
ATOM 3 OP2 G A 1 52.137 49.542 50.511 1.00 99.21 O
ATOM 4 O5' G A 1 50.161 49.136 52.023 1.00 99.82 O
ATOM 5 C5' G A 1 50.216 49.948 53.210 1.00 98.63 C
ATOM 6 C4' G A 1 50.968 49.231 54.309 1.00 97.84 C
ATOM 7 O4' G A 1 50.450 47.888 54.472 1.00 97.10 O
ATOM 8 C3' G A 1 52.454 49.030 54.074 1.00 98.07 C
ATOM 9 O3' G A 1 53.203 50.177 54.425 1.00 99.39 O
ATOM 10 C2' G A 1 52.781 47.831 54.957 1.00 96.96 C
ATOM 11 O2' G A 1 53.018 48.156 56.313 1.00 96.77 O
ATOM 12 C1' G A 1 51.502 47.007 54.836 1.00 95.70 C
ATOM 13 N9 G A 1 51.628 45.992 53.798 1.00 93.67 N
ATOM 14 C8 G A 1 51.064 46.007 52.547 1.00 92.60 C
ATOM 15 N7 G A 1 51.379 44.966 51.831 1.00 91.19 N
ATOM 16 C5 G A 1 52.197 44.218 52.658 1.00 91.47 C
ATOM 17 C6 G A 1 52.848 42.992 52.425 1.00 90.68 C
ATOM 18 O6 G A 1 52.826 42.291 51.404 1.00 90.38 O
ATOM 19 N1 G A 1 53.588 42.588 53.534 1.00 90.71 N
ATOM 20 C2 G A 1 53.685 43.282 54.716 1.00 91.21 C
ATOM 21 N2 G A 1 54.452 42.733 55.671 1.00 91.23 N
ATOM 22 N3 G A 1 53.077 44.429 54.946 1.00 91.92 N
ATOM 23 C4 G A 1 52.356 44.836 53.879 1.00 92.62 C
ATOM 24 P C A 2 54.635 50.420 53.741 1.00100.19 P
ATOM 25 OP1 C A 2 55.145 51.726 54.238 1.00100.19 O
OP3¶
The first residue will have only OP1 and OP2 (OP3 will be removed):
ATOM 1 OP3 G A 1 50.193 51.190 50.534 1.00 99.85 O
ATOM 2 P G A 1 50.626 49.730 50.573 1.00100.19 P
ATOM 3 OP1 G A 1 49.854 48.893 49.562 1.00100.19 O
ATOM 4 OP2 G A 1 52.137 49.542 50.511 1.00 99.21 O
ATOM 5 O5' G A 1 50.161 49.136 52.023 1.00 99.82 O
ATOM 6 C5' G A 1 50.216 49.948 53.210 1.00 98.63 C
ATOM 7 C4' G A 1 50.968 49.231 54.309 1.00 97.84 C
Listing. An example: 1ehz.pdb.
