AddH: pretend missing N-terminal MET doesn't exist

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Another thing that's come up while looking at 6zm7. Very minor in the grand scheme of things, but might be a nice touch: this model has numerous chains that include the N-terminal MET in the deposited sequence, but where the density and surrounding context clearly show that it's removed in the final protein. I realise that this is an error on the part of the depositors, but I suspect it's a common one. Might be worth adding a simple heuristic to AddH: if the sequence includes the N-terminal MET but the model starts at residue 2, treat residue 2 as an N-terminus anyway. In situations like this it'll improve the model; in situations where the N-terminal MET is unmodelled because it's poorly resolved, it's unlikely to make anything worse.

OpenGL version: 3.3.0 NVIDIA 450.51.05
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         12G         37G        247M         12G         49G
	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: 5.12.8

[pett]

I dunno, it seems unwise to me to put in a specific heuristic that takes data explicitly present in the input and assumes it's wrong. It would seem better that in scenarios where density or other data indicates that the chain sequence is wrong, _then_ adjust the sequence. ISOLDE could do this when it identifies this problem with this code to drop the first residue/letter of the chain:

chain.bulk_set(chain.residues[1:], chain.characters[1:])

--Eric