- BUGS:
motm full size images sometimes have composite-number with multiple composites. This is not handled currently and the image can be blank. e.g.: 75-TissueFactor-2hft-composite-0.png 64-Kinesin-3kin-composite-0.png Appears to be just these two entries for now.
- IDEA
lysozyme "movie" - sequence through the various work at UofO on lysozyme variants!! sept 2000
TODO:
add bonds for HETATM - keep getting complaints about no bonds for heavy atoms
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Decision: throw out OXT, O5T, and O3T atoms - no bond info http://deposit.rcsb.org/adit/docs/pdb_atom_format.html Terminal oxygen atoms are presented as OXT for proteins, and as O5T or O3T for nucleic acids.
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Decision: toss alternate locations (only take the "A" atoms) but this is not guaranteed to be the "best" per this email on the list:
My understanding of the alternative locations was different---that is that alternative locations were not necessarily consistently named. That is, there is no guarantee that taking just the "A" locations gives you a consistent model. https://lists.sdsc.edu/pipermail/pdb-l/2006-July/003420.html
Interesting test cases:
- 1AEW - cadmium (CD) atoms with bonds - interesting (and smaller PDB file)
- 1IDR (one eye Dee ahr) - missing oxygen in path - crashes viewer
- 1B89 - a couple of orphan atoms (Residues with only one atom)
- 1CD3 - funny dotted connection on backbone
HUGE test cases:
- 1BGL - very big - two complexes
Other:
1BGW:
E/ParserPdbFile: Alternate location indicator is B, skipppi
E/ParserPdbFile: matchBonds file: 1bgw no CHARMM entry for atom 6075 residue ALA type N
/ParserPdbFile: connectResidues: excessive bond dist = 1.33from atom 2144 to 2155
depends on preloaded pdb files in name.pdb.gz format. The dir on the device queried is:
/storage/emulated/0/PDB/ - i.e. the PDB folder at the root directory
vim reverse order of lines https://vim.fandom.com/wiki/Reverse_order_of_lines
:g/^/m0