Missing bonds in mmCIF 1tna

[Tom Goddard]

Opening 1tna mmCIF is missing many backbone bonds. (And the missing bonds confuse smart display which ends up showing nothing.)

open 1tna
show
view

It displays correctly in Chimera 1. Also the PDB format file for 1tna has the backbone bonds.

open 1tna format pdb

[Greg Couch]

There are two bugs here. One is that nothing is displayed when the structure is opened -- you have to 'show' and 'view' before you can see anything. The other bug is that even if you do that, the backbone bonds are 'missing segments' because the atom names are the obsolete O3* instead of O3'. If the atom names are updated, then it displays correctly.

So what to do? 1tna is an obsolete entry and ChimeraX tells the user that in the log. Scanning the atom names to replace the *'s will take additional time and is not needed for current mmCIF files from the PDB. We don't know how prevalent mmCIF files are with * atom names. Is it worth it?

[Greg Couch]

Decided to replace * with ' in atom names in mmCIF files to handle these old mmCIF files that are still available from the PDB.

[pett]

reducing # of categories, so lumping into I/O category