id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3168	Support CHARMM/X-PLOR format PDB files	Tristan Croll	Eric Pettersen	"Like it or not, these are still a favourite with many in the molecular dynamics world - probably because it was the oldest and least-hacky way to support really large models within the PDB format. It essentially ignores the chain ID, instead using the SEGID field (4 characters) to separate chains. As a consequence, many such files will have multiple residues with identical chain ID and number, but different SEGID. Other adaptations that I know of are in the atom numbering: beyond 99999 VMD/NAMD first switch to hexadecimal, and if it gets beyond the limit of that just fills the atom number field with ***** from that point on.

One approach to supporting it that I think would be ""easy"": simply replace chain ID with SEGID throughout the model. To trigger it you could ask the user to explicitly specify ""format xplor"" when opening, or perhaps watch for the case where SEGIDs are used and a duplicate chain ID/resnum is encountered (although I imagine that would slow things down a lot). I wouldn't worry about *saving* to the format - the result would be perfectly compatible with mmCIF.

Entirely understand if you don't want to support it - but if there's an easy way, it might be worthwhile.

Will attach an example (protein chains are uniquely named/numbered relative to each other, but glycans share the same chain IDs as their proteins and are numbered from 1). This is different from the one I mentioned yesterday - turns out the X-PLOR format had nothing to do with its issues on loading into ChimeraX, and everything to do with the fact that beyond chain A every single atom came with its own TER... honestly one of the stranger things I've come across:

{{{
ATOM  20374 H5_5 F2A A1179      26.834 -12.437 -82.219  1.00  0.00           H  
ATOM  20375 H5_6 F2A A1179      26.003  -8.493 -86.927  1.00  0.00           H  
ATOM  20376 H5_7 F2A A1179      28.310 -25.830 -77.706  1.00  0.00           H  
ATOM  20377 H5_8 F2A A1179      34.986 -24.667 -81.395  1.00  0.00           H  
ATOM  20378 H5_9 F2A A1179      40.367 -26.088 -78.035  1.00  0.00           H  
TER   20379      ACE B  26
ATOM  20380  C   ACE B  26     -36.536  40.158  14.798  1.00  0.00           C  
TER   20381      ACE B  26
ATOM  20382  O   ACE B  26     -36.454  38.949  14.564  1.00  0.00           O  
TER   20383      ACE B  26
ATOM  20384  CH3 ACE B  26     -36.819  40.560  16.168  1.00  0.00           C  
TER   20385      ACE B  26
ATOM  20386 HH31 ACE B  26     -37.494  39.806  16.573  1.00  0.00           H  
TER   20387      ACE B  26
ATOM  20388 HH32 ACE B  26     -35.891  40.639  16.734  1.00  0.00           H  
TER   20389      ACE B  26
ATOM  20390 HH33 ACE B  26     -37.349  41.511  16.235  1.00  0.00           H  
TER   20391      ALA B  27
ATOM  20392  N   ALA B  27     -36.215  41.146  13.953  1.00  0.00           N  
}}}
 "	enhancement	closed	moderate		Input/Output		fixed						all	ChimeraX