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Getting Started: I want to ...

fetch a structure from the PDB database


$ --fetch 1xjr
downloading...1xjr ok

fetch a biologicaly assembly


$ --fetch_ba 1xjr
downloading...1xjr_ba.pdb ok

or over a list of pdb ids in a text file:

$ cat data/pdb_ids.txt

$ while read p; do --fetch_ba $p; done < data/pdb_ids.txt
downloading...1y26_ba.pdb ok
downloading...1fir_ba.pdb ok

$ ls *.pdb
1fir_ba.pdb 1y26_ba.pdb

get sequences of a bunch of PDB files

Example: --get_seq *.pdb
# 1xjr
> A:1-47
# 6TNA
> A:1-76
# rp2_bujnicki_1_rpr
> A:1-15
> B:1-10
> C:1-15
> D:1-10
> E:1-15
> F:1-10
> G:1-15
> H:1-10

get secondary structures of your PDB files

.. automodule::

delete a part of of your structure


$ for i in *pdb; do --delete A:46-56 $i > ../rpr_rm_loop/$i ; done

go over all files in the current directory, remove a fragment of chain A, residues between 46-56 (including them) and save outputs to in the folder rpr_rm_loops.

get numbering of your structure and rename chains

Rename chain B in structure 4_das_1_rpr.pdb:

$ --get_seq  4_das_1_rpr.pdb
> 4_das_1_rpr.pdb B:1-126
$ --edit 'B:1-126>A:1-126' 4_das_1_rpr.pdb > 4_das_1_rpr2.pdb
$ --get_seq  4_das_1_rpr2.pdb
> 4_das_1_rpr2.pdb A:1-126

edit your structure (rename chain)


$ --edit 'A:3-21>A:1-19' 1f27_clean.pdb > 1f27_clean_A1-19.pdb

or even:

$ --edit 'A:3-21>A:1-19,B:22-32>B:20-30' 1f27_clean.pdb > 1f27_clean_renumb.pdb

or even, even, do rename X chain to A only for Chen's pdb structures in the folder, in place (so don't create a new file):

for i in *Chen*; do --edit 'X:1-125>A:1-125' $i > ${i}_temp; mv ${i}_temp ${i}; done
# do only edit for Chen's pdb structures, in place.

find missing atoms in my structure


$ --get_rnapuzzle_ready input/1_das_1_rpr_fixed.pdb
HEADER Generated with rna-pdb-tools
HEADER ver 91ed4f8-dirty
HEADER Sun Mar  5 10:58:07 2017
REMARK 000 Missing atoms:
REMARK 000  + P B <Residue C het=  resseq=1 icode= > residue # 1
REMARK 000  + OP1 B <Residue C het=  resseq=1 icode= > residue # 1
REMARK 000  + OP2 B <Residue C het=  resseq=1 icode= > residue # 1
REMARK 000  + O5' B <Residue C het=  resseq=1 icode= > residue # 1
ATOM      1  P     C A   1     -16.936  -3.789  68.770  1.00 11.89           P
ATOM      2  OP1   C A   1     -17.105  -3.675  67.302  1.00 14.35           O
ATOM      3  OP2   C A   1     -15.666  -4.265  69.342  1.00 12.68           O

mutate residues

For example, to replace the first four residues of chain A into adenines and 13th A of chain B, run: --mutate 'A:1A+2A+3A+4A,B:13A' \
   --inplace output/205d_rmH2o_mutA1234-B1_inplace.pdb


Figure. Input structure on the left, mutated structure on the right.

If, for whatever reason, the tool here does not do what you want, use the tool from MC-Fold|MC-Sym Pipeline (go there and scroll down to the Section: "RNA SEQUENCE MUTATION" at the very bottom of the page).

Moreover, you can also mutate interactively proteins and nucleic acids with PyMOL >2.


Learn more here

If you want to mutate with PyMOL with command-line see this

add missing atoms

The tool is using the function:

.. automethod:: rna_tools.rna_tools_lib.RNAStructure.get_rnapuzzle_ready
You can’t perform that action at this time.