addh: metal-clash proton stripping

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.92 (2020-03-05)
Description
AddH doesn't add a hydrogen to the peptide bond of Cys B77 in 3r24. The map is clear hera and the geometry is correct: the amide points directly at the sulfur of Cys74, not at the nearby zinc ion.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-03-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3r24 structureFactors true

Summary of feedback from opening 3r24 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3r24 from
http://files.rcsb.org/download/3r24.cif  
Fetching compressed 3r24 structure factors from
http://files.rcsb.org/download/3r24-sf.cif  
Resolution: 2.0  
  
3r24 title:  
Crystal structure of nsp10/nsp16 complex of SARS coronavirus" if possible
[more info...]  
  
Chain information for 3r24  
---  
Chain | Description  
1.1/A | 2'-O-methyl transferase  
1.1/B | Non-structural protein 10 and Non-structural protein 11  
  
Non-standard residues in 3r24 #1.1  
---  
SAM — S-adenosylmethionine  
ZN — zinc ion  
  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> view :SAM

> addh

Summary of feedback from adding hydrogens to 3r24 #1.1  
---  
warning | Not adding hydrogens to /B HIS 9 CB because it is missing heavy-atom
bond partners  
notes | Termini for 3r24 (#1.1) chain A determined from SEQRES records  
Termini for 3r24 (#1.1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLN 3, /B HIS 9  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ILE 294, /B SER 129  
1730 hydrogen bonds  
Adding 'H' to /A GLN 3  
Adding 'H' to /B HIS 9  
/A ILE 294 is not terminus, removing H atom from 'C'  
/B SER 129 is not terminus, removing H atom from 'C'  
4111 hydrogens added  
  

> hide HC

> select #1

7812 atoms, 7419 bonds, 8 pseudobonds, 25 models selected  

No template found for residue B77 (CYS)  

Doing nothing  
Updating bulk solvent parameters...  

> addh metalDist 1

Summary of feedback from adding hydrogens to 3r24 #1.1  
---  
warning | Not adding hydrogens to /B HIS 9 CB because it is missing heavy-atom
bond partners  
notes | Termini for 3r24 (#1.1) chain A determined from SEQRES records  
Termini for 3r24 (#1.1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLN 3, /B HIS 9  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ILE 294, /B SER 129  
981 hydrogen bonds  
/A ILE 294 is not terminus, removing H atom from 'C'  
/B SER 129 is not terminus, removing H atom from 'C'  
2 hydrogens added  
  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

The added-hydrogen-to-metal distance of 2.955 for Cys B77 is beginning to wander into the grey area of metal-coordination distances. The distance criteria _was_ a parent-atom-to-metal distance of 3.6. Given the smaller radius of hydrogen and that the upper 2s is on the back side of the coordination-distance bell curve, I have changed the criteria to a H-to-metal distance of 2.7. That rectifies this situation as well as a similar situation with Cys B 120 in the same structure.

--Eric