I’ve had one or two discussions with colleagues about transferring values shown in annotation tracks in a Jalview alignment to Pymol or Chimera, and was wondering whether anyone had any suggestions on how we could improve support in Jalview for this ?
In addition to Jalview’s linkage to Pymol and Chimera/X, which allows colours on the alignment to be mapped to linked 3D structures, Jalview also provides a CSV export option for annotation tracks, allowing them to be more easily parsed by pymol or chimera/x scripts.
Although not for annotations, Jalview does provide a way to read or write sequence features as attributes in Chimera/X and Pymol. We can certainly implement a similar capability for annotation tracks associated with sequences, perhaps also even allowing alignment tracks (like conservation) to be transferred to individual chains - but I’m also wondering if there are other forms of data transfer you might want.
Looking forward to comments or suggestions !