Workflows

Example #1

The native:

[mq] md_1msy_clx cat 1msy_clean.pdb.outCR
Classifier: Clarna
chains:  A 2647 2673
A 2648   A 2672          bp G U                  WW_cis   0.8732
A 2649   A 2671          bp C G                  WW_cis   0.9160
A 2650   A 2670          bp U A                  WW_cis   0.9289
A 2651   A 2669          bp C G                  WW_cis   0.9439
A 2652   A 2668          bp C G                  WW_cis   0.9281
A 2655   A 2656          bp G U                  SH_cis   0.9227
A 2656   A 2665          bp U A                 WH_tran   0.8526
A 2657   A 2664          bp A G                 HS_tran   0.8513
A 2658   A 2663          bp C G                  WW_cis   0.9421
A 2659   A 2662          bp G A                 SH_tran   0.7619

but analyzed structres are like:

[mq] md_1msy_clx cat struc/1msy_rnakbmd_decoy1478_clx.pdb.outCR
Classifier: Clarna
chains: A 1 27
 2       26          bp G U                  WW_cis   0.7196
 3       25          bp C G                  WW_cis   0.6702
 4       24          bp U A                  WW_cis   0.8911
 5       23          bp C G                  WW_cis   0.8925
 6       22          bp C G                  WW_cis   0.9026
 9       10          bp G U                  SH_cis   0.8714
 10       19          bp U A                 WH_tran   0.7279
 11       18          bp A G                 HS_tran   0.8810
 12       17          bp C G                  WW_cis   0.9115

You have to renumber 1msy_clean.pdb to 1:27:

$ rna_pdb_tools.py --edit 'A:2647-2673>A:1:17' 1msy_clean.pdb > 1msy_clean_renumb.pdb
_images/edit.png

Example #2

Listing:

$ rna_pdb_tools.py --get_seq 1nuj_rnakbmd_decoy1000_clx.pdb
> 1nuj_rnakbmd_decoy1000_clx.pdb A:1-13
CGGACCGAGCCAG
> 1nuj_rnakbmd_decoy1000_clx.pdb B:14-24
GCUGGGAGUCC

$ rna_pdb_tools.py --get_seq 1nuj_clean.pdb
> 1nuj_clean.pdb A:18-30
CGGACCGAGCCAG
> 1nuj_clean.pdb B:39-49
GCUGGGAGUCC

$ rna_pdb_tools.py --edit 'A:18-30>A:1-13,B:39-49>B:14-24' 1nuj_clean.pdb > 1nuj_clean_renumber.pdb

$ rna_pdb_tools.py --get_seq 1nuj_clean_renumber.pdb
> 1nuj_clean_renumber.pdb A:1-13
CGGACCGAGCCAG
> 1nuj_clean_renumber.pdb B:14-24
GCUGGGAGUCC

Example #3

Starting structure doesn’t have chain id:

# add chain A
$ parallel "rna_add_chain.py -c A {} > ../struc_with_chain/{}" ::: *.pdb
# edit the second part of the new chain A as B
$ parallel "rna_pdb_gtools.py --edit 'A:14-27>B:14-27' {} > out/{}" ::: *.pdb
_images/1duq.png