Added NH2 saved after TER

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
If I add a C-terminal NH2 to a chain (by using "isolde add ligand NH2" which builds a new residue with the correct chain ID but wrong (for this purpose) number, then renumbering the residue to the correct chain ID and adding the bond to the preceding C), when I save the result as a PDB the NH2 ends up with all the other ligands (i.e. after the TER). If I open a model like 1sle (with a C-terminal NH2 on chain M) and save it to PDB, it's correctly written before the TER. What am I missing here?

OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        4.6G         47G        233M         10G         57G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
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[Eric Pettersen]

Does the NH2 immediately follow the previously C-terminal residue in the residue list?

[Tristan Croll]

The add-ligand code just adds the residue using default parameters (so it ends up at the end of model.residues​). I haven't done anything explicit to re-order it.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 12 November 2020 18:18
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3929: Added NH2 saved after TER

#3929: Added NH2 saved after TER
----------------------------------------+----------------------------
          Reporter:  Tristan Croll      |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  feedback
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Does the NH2 immediately follow the previously C-terminal residue in the
 residue list?

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3929#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Seems like I need the code that incorporates residues into a chain to also reorder the global residue list; otherwise on output those residues will be treated like bound ligands.

[Eric Pettersen]

structure with NH2 before bond to chain is formed

[Eric Pettersen]

Hi Tristan,

I've attached a session to this ticket with a structure with an NH2 residue in it not yet bonded to a chain. If I bond it to the C-terminus of chain C with "bond /c:141@c #1:nh2@n reasonable false" it shows up in the chain sequence properly (sequence chain #1/c). If I then save a PDB file the NH2 is located at the end of the C chain with no intervening TER card. I don't know how/where this procedure differs from what you are doing.

--Eric

[Eric Pettersen]

Presumably the same as #3892; fixed by using struct_edit.add_bond() in lieu of just new_bond()