AddH: unusual positioning

[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
AddH occasionally comes up with somewhat weird geometry on nucleotides... this is adenosine chain L5, residue 243 of 6zm7.

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        7.7G         45G        219M        9.9G         54G
	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
File attachment: rna_weird_h.jpg

rna_weird_h.jpg​

[Tristan Croll]

Added by email2trac

[Tristan Croll]

And L5 residue 1907 has the N6 atom with hydrogens tetrahedral like a 
primary amine.

On 2020-08-02 16:25, ChimeraX wrote:

[pett]

For L5:243, it's positioning one hydrogen to H-bond with /L5:242@O4 and the other to H-bond with /L5:196@N3. If you turn off hbond-guided addition, the protons are put in their "normal" quasi-planar positions.

[pett]

For /L5:1907, one proton is positioned to H-bond with /L5:1885@O2' and the other with both /L5:2068@O2 and /L5:1908@N6.

Aniline (​https://en.wikipedia.org/wiki/Aniline) does have some flexibility in the positioning of its protons. Whether it has this much flexibility, I dunno. Keeping it this way until proven otherwise. :-)