Deleted bond reappears in saved mmCIF file

[Asmit Bhowmick <abhowmick@…>]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202405132341 (2024-05-13 23:41:14 UTC)
Description
Deleting a bond from 7rf1 (residue OEX, atoms O5 - MN1) then saving a new mmcif and reloading and the bond reappears.

Log:
UCSF ChimeraX version: 1.9.dev202405132341 (2024-05-13)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7rf1

Summary of feedback from opening 7rf1 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /L:1  
Atom H1 is not in the residue template for MET /Z:1  
Atom H1 is not in the residue template for MET /z:1  
  
7rf1 title:  
RT XFEL structure of Photosystem II averaged across all S-states at 1.89
Angstrom resolution [more info...]  
  
Chain information for 7rf1 #1  
---  
Chain | Description | UniProt  
A a | Photosystem II protein D1 1 | PSBA1_THEEB 1-344  
B b | Photosystem II CP47 reaction center protein | PSBB_THEEB 1-510  
C c | Photosystem II CP43 reaction center protein | PSBC_THEEB 13-473  
D d | Photosystem II D2 protein | PSBD_THEEB 1-352  
E e | Cytochrome b559 subunit alpha | PSBE_THEEB 1-84  
F f | Cytochrome b559 subunit beta | PSBF_THEEB 1-45  
H h | Photosystem II reaction center protein H | PSBH_THEEB 1-66  
I i | Photosystem II reaction center protein I | PSBI_THEEB 1-38  
J j | Photosystem II reaction center protein J | PSBJ_THEEB 1-40  
K k | Photosystem II reaction center protein K | PSBK_THEEB 1-46  
L l | Photosystem II reaction center protein L | PSBL_THEEB 1-37  
M m | Photosystem II reaction center protein M | PSBM_THEEB 2-36  
O o | Photosystem II manganese-stabilizing polypeptide | PSBO_THEEB -25-246  
R r | Photosystem II protein Y | PSBY_THEEB 1-41  
T t | Photosystem II reaction center protein T | PSBT_THEEB 2-32  
U u | Photosystem II 12 kDa extrinsic protein | PSBU_THEEB -29-104  
V v | Cytochrome c-550 | CY550_THEEB -25-137  
X x | Photosystem II reaction center X protein | PSBX_THEEB 1-41  
Y y | Photosystem II reaction center protein Ycf12 | YCF12_THEEB 1-46  
Z z | Photosystem II reaction center protein Z | PSBZ_THEEB 1-62  
  
Non-standard residues in 7rf1 #1  
---  
BCR — β-carotene  
BCT — bicarbonate ion  
CL — chloride ion  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE2 — Fe (II) ion  
FME — N-formylmethionine  
HEC — heme C  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
STE — stearic acid  
  
156 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> delete ~:OEX

> delete ~/A:OEX

> delete atoms sel

> delete bonds sel

> save /Users/goddard/Desktop/test.cif

> open test.cif

> hide #2 models




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[Tom Goddard]

The OEX ligand template from RCSB has the O5 - MN1 bond, so maybe it is unreasonable to expect you can delete a bond from the residue, save mmCIF, and not have it restore the bond when reloaded since the mmCIF files in general don't include the bonds and rely on residue templates to create the bonds.

But I'll let Greg judge if he thinks this should work (bond stays deleted) or not.

[pett]

Works correctly via PDB format because the PDB file contains CONECT records instead of using templates.

[Greg Couch]

For this to work, after the bond is deleted and before the mmCIF file is saved, the name of the residue needs to be changed to be something without a template (and not UNK).