Ignore iffy CONECT records

[Tristan Croll]

When writing PDB, should generate SSBOND/LINK records based on the cross-residue bonds in the structure and ignore those records in the metadata

[tic20@…]

(most closely related to this ticket)

It looks like the weird bonding issue was due to me editing the PDB file 
outside of ChimeraX without clearing the CONECT records. I did this 
again (extending some helices that are resolved in the map, but hadn't 
been built yet), and when I reopened the chain-break pseudobonds were 
all in the wrong places and AddH created a spurious terminus (NH3/COOH) 
in the middle of a chain.

On the one hand, this is my fault and can (fairly) easily be avoided by 
some scripting (adding the new residues directly into the model in 
ChimeraX rather than hacking in a text editor). On the other hand, this 
approach of piecing together PDB files (renumber the residues and change 
the chain ID if necessary, then copy/paste into the right place in a 
text editor) has always been quite popular in the model-building 
community. I'll leave it to you to decide whether or not it should be 
catered to.

On 2019-05-29 00:36, ChimeraX wrote:

[pett]

SSBOND/LINK records are now generated that correspond to the structure.

As for hand-editing mishaps, if there were some actual concrete suggestion I would consider it. I don't know of a good way to tell if CONECT records are "bad". Missing serial numbers isn't good enough, people delete parts of files all the time while leaving the rest alone. I am open to non-crazy ideas.

[tic20@…]

Well, one dead giveaway is that if someone has hand-edited the PDB file the atom serial numbers will be non-sequential - a sudden jump upwards for a deletion or a section numbered from 1 for an insertion. I’d think that Invalidating all CONECT records past that point should catch just about every case.
 

[pett]

Given that the automatically connectivity generation is pretty good, it would probably be okay to ignore CONECT/LINK records when there are jumps in the serial numbers, or any CONECT record lists missing serial numbers.