Unrecognized field name "res_tag".

[JosephHeili]

initialize_drawing ('3nkb.pdb');

ans =

'3NKB_1 A:1-9 B:1-64'

Drawing helices... done
Moving graphic elements to back... could take a while.
Elapsed time is 0.000430 seconds.

Unrecognized field name "res_tag".

Error in setup_motifs (line 50)
setappdata( gca, residue.res_tag, residue );

Error in initialize_drawing (line 50)
setup_motifs( motifs );

get_res_tags.m
Unable to resolve the name 'get_res_tags.m'.

get_res_tags.m
Unable to resolve the name 'get_res_tags.m'.

[JosephHeili]

This is using the output files from the online RNA_info tool from https://rosie.graylab.jhu.edu/rna_info

[rhiju]

Thanks for posting the issue -- the file that is reported as missing should be in RiboDraw/scripts/selections/get_res_tags.m

You may need to redo the "Set Path" command to "Add with subfolders..." in RiboDraw/scripts.

Even with that fix, you may run into issues.
I tried to run ribodraw with 3NKB.pdb downloaded from the PDB and I did find a couple issues:

1. The FASTA file was not output by the server https://rosie.graylab.jhu.edu/rna_info

2. The command initialize_drawing('114885-3nkb-start_pdb'); dies with:

Error using get_resnum_from_tag
Too many input arguments.

Error in get_sequence (line 19)
[resnum,chains,segid] = get_resnum_from_tag( fasta.Header );

Error in initialize_drawing (line 22)
[sequence,resnum,chains,segid,non_standard_residues] = get_sequence( [tag,'.fasta']);

The issue, IIRC, is that RiboDraw only handles RNA's that are single chains at the moment.

Did you see similar issues or others? If similar issues, we can try to put in fixes, or at the very least, better warnings =).

[JosephHeili]

Thanks so much for the reply. I also noticed that the FASTA file was not output by ROSIE, I had to download that from RCSB.org with the PDB file and then edit the format in the FASTA file to match what RiboDraw script was expecting to find.

I will try resetting the path, though I did "add with subfolders" intially. I fear you are correct that if RiboDraw can only handle a single chain then I will not get HDV to work. Maybe I can ditch the target strand. I'll report back after tinkering and thanks again for the reply!

[JosephHeili]

I'll have to look into how this example was run, since it looks like tC19Z has two chains: https://github.com/ribokit/RiboDraw/blob/master/drawings/ribozymes/tC19Z/tC19Z.fasta

[everyday847]

The Rosie server definitely used to produce the fasta. I'll see if there's an easy fix. (if you're able to install Rosetta yourself, these tools are also dirt cheap to run locally)