RNA Puzzle Submission

The RNA Puzzle organizers required ONE file with your submissions in the NMR-style multiple model PDB format.

First, prepare your structures in the folder and run to get them RNApuzzle ready (_rpr):

$ for i in *.pdb; do rna_pdb_toolsx.py --get_rnapuzzle_ready $i > ${i/.pdb/_rpr.pdb}; done

merge them as one file in the order as you like (or use *):

$ rna_pdb_merge_into_one.py 02_19pz_v1_SimRNA3.22_thrs6.60A_clust02-000001_AA_out_rpr.pdb \
09_19pz_v2_SimRNA3.22_thrs6.60A_clust03-000001_AA_out_rpr.pdb \
d311d821-a075-4df0-bd7d-1dcf7669dad9_ALL_thrs6.20A_clust01-000001_AA_out_rpr.pdb \
d311d821-a075-4df0-bd7d-1dcf7669dad9_ALL_thrs6.20A_clust03-000001_AA_out_rpr.pdb \
05_19pz_v1_SimRNA4.xx_thrs6.60A_clust02-000001_AA_out_rpr.pdb  > rp19_bujnicki.pdb

and verify your file with the template provided by the organizers (if provided)::

$ diffpdb --method diff Reference_19.pdb rp19_bujnicki.pdb
#<empty = no difference but xyz columns, OK!>

diffpdb is a part of the rna-pdb-tools package.

_images/rp19.png

In terminal:

$ head -n 5 Reference_19.pdb rp19_bujnicki.pdb
==> Reference_19.pdb <==
MODEL        1
ATOM      1  P     G A   1       0.000   0.000   0.000  1.00  0.00           P
ATOM      2  OP1   G A   1       0.000   0.000   0.000  1.00  0.00           O
ATOM      3  OP2   G A   1       0.000   0.000   0.000  1.00  0.00           O
ATOM      4  O5'   G A   1       0.000   0.000   0.000  1.00  0.00           O
==> rp19_bujnicki.pdb <==
MODEL        1
ATOM      1  P     G A   1      31.463  14.180  -0.676  1.00  0.00           P
ATOM      2  OP1   G A   1      31.412  12.806  -1.223  1.00  0.00           O
ATOM      3  OP2   G A   1      30.646  15.083  -1.517  1.00  0.00           O
ATOM      4  O5'   G A   1      30.955  14.212   0.842  1.00  0.00           O

$ tail -n 5 Reference_19.pdb rp19_bujnicki.pdb
==> Reference_19.pdb <==
ATOM   1325  C5    C B  22       0.000   0.000   0.000  1.00  0.00           C
ATOM   1326  C6    C B  22       0.000   0.000   0.000  1.00  0.00           C
TER    1327        C B  22
ENDMDL
END
==> rp19_bujnicki.pdb <==
ATOM   1325  C5    C B  22      29.927  21.506  -6.542  1.00  0.00           C
ATOM   1326  C6    C B  22      29.822  22.338  -5.500  1.00  0.00           C
TER    1327        C B  22
ENDMDL
END