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_tools.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-tools package.
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
The Bujnicki lab is using this script to process the results and send the results, you can hack it for your own case:
[mm] rnapuzzle_sender$ git:(master) ✗ ./rnapuzzle_sender.py
rnapuzzle_sender
Usage: rnapuzzle_sender.py
Options:
-h, --help show this help message and exit
-d DIR, --dir=DIR
-s EMAIL_SUBJECT, --email_subject=EMAIL_SUBJECT
email subject
File: rna-tools/rna_tools/tools/rnapuzzle_sender.