Known Issues

Annotation and numbering issues

[SOLVED] Some GDPs that are listed as HETATMs in the mmCIF files are not detected correctly to be real nucleotides. (e.g. 1e8o-E)
Some chains are truncated in different pieces with different chain names. Reason unknown (e.g. 6ztp-AX)
[SOLVED] Some chains are not correctly renamed A in the produced separate files (e.g. 1d4r-B)

[SOLVED] Chain names appear in triple in the FASTA header (e.g. 1d4r[1]-B 1d4r[1]-B 1d4r[1]-B)

Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
Weight sequences in alignment to give more importance to rarer sequences
Give both gap_percent and insertion_gap_percent
A field estimating the quality of the sequence alignment in table family.
Possibly, more metrics about the alignments coming from Infernal.
Run cmscan ourselves from the NDB instead of using Rfam-PDB mappings ? (Iff this actually makes a real difference, untested yet)
Use and save Infernal alignment bounds and truncation information
Save if a chain is a representative or not in BGSU list, so that they can be filtered easily
Annotate unstructured regions (on a nucleotide basis)

cmalign --merge is now deprecated, we use esl-alimerge instead. But, esl is a single-core process. We should run the merges of alignements of different families in parallel to save some time [TODO].