swapaa to GLY: Cannot identify backbone

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202105180049 (2021-05-18 00:49:36 UTC)
Description
It seems strange that swapaa cannot swap glycine /G:44 for glycine.  Why you ask?  I was running a script that swapped every residue with the same type to complete the side chains.  The error message is a bit unclear "Cannot identify backbone".  /G:44 has a C, CA and N atom but no O atom.  I guess the error has something to do with the missing O atom?  The documentation doesn't say what backbone atoms are needed.

Log:
UCSF ChimeraX version: 1.3.dev202105180049 (2021-05-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6o9z format mmcif fromDatabase pdb

6o9z title:  
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B
bound to eukaryotic translation initiation factor 2 from Homo sapiens [more
info...]  
  
Chain information for 6o9z #1  
---  
Chain | Description  
A B | Translation initiation factor eIF-2B subunit ε  
C D | Translation initiation factor eIF-2B subunit β  
E F | Translation initiation factor eIF-2B subunit δ  
G H | Translation initiation factor eIF-2B subunit α  
I J | Translation initiation factor eIF-2B subunit γ  
L M | Eukaryotic translation initiation factor 2 subunit 1  
  

> swapaa /G:44 GLY

Using Dunbrack library  
Swapping /G GLY 44 to GLY  
  
Cannot identify backbone of residue /G GLY 44)  

> select /G:45

5 atoms, 4 bonds, 1 residue, 1 model selected  

> view sel




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[goddard@…]

A missing O backbone atom only seems to cause swapaa to fail when adding GLY.  I deleted O from residue /G:45 and swapaa still worked on it if I convert it to LEU but failed it I tried to add GLY.

[Tom Goddard]

If you don't expect to fix it for a long time (priority low) maybe worth putting in the documentation that swapaa to GLY only works if the O backbone atom is present.

[Elaine Meng]

swapaa to gly is kinda ridiculous anyway, since you could just delete the sidechain (gly is the one with no sidechain)