AddH: N-linked glycans

[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 (2020-03-08)
Description
Would it be possible for AddH to make an exception to its geometry-based inference approach for assigning bonds to N-linked glycans? Some refinement methods lately seem to be making these *seriously* wonky (some coming out almost linear), so AddH skips adding a hydrogen to the Asn ND2 and NAG C1. For a (actually not particularly extreme) example see C282 of 6vsb.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-03-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6vsb

6vsb title:  
Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain
up [more info...]  
  
Chain information for 6vsb #1  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6vsb #1  
---  
NAG — N-acetyl-D-glucosamine  
  
  

> open 21375 fromDatabase emdb

Opened emd_21375.map, grid size 432,432,432, pixel 1.05, shown at level
0.0501, step 2, values float32  

> clipper associate #2 toModel #1

6vsb title:  
Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain
up [more info...]  
  
Chain information for 6vsb  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C | Spike glycoprotein  
  
Non-standard residues in 6vsb #1.1  
---  
NAG — N-acetyl-D-glucosamine  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> set bgColor white

> sequence chain /A

Alignment identifier is 1.1.A  

> view sel

> addh

Summary of feedback from adding hydrogens to 6vsb #1.1  
---  
warnings | Not adding hydrogens to /A SER 60 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A PHE 79 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASN 81 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A PHE 135 CB because it is missing heavy-atom bond
partners  
178 messages similar to the above omitted  
notes | Termini for 6vsb (#1.1) chain A determined from SEQRES records  
Termini for 6vsb (#1.1) chain B determined from SEQRES records  
Termini for 6vsb (#1.1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A ALA 27, /A PHE 79, /A
ASN 99, /A GLU 156, /A LYS 187, /A GLY 261, /A LEU 335, /A TYR 449, /A PRO
491, /A VAL 503, /A SER 640, /A VAL 687, /A ARG 815, /A GLN 853, /B ALA 27, /B
ASN 81, /B SER 155, /B LYS 187, /B PRO 217, /B ALA 263, /B TYR 449, /B ASN
460, /B ASN 487, /B VAL 503, /B THR 638, /B VAL 687, /B ARG 815, /B GLN 853,
/C ALA 27, /C ASP 80, /C ASN 99, /C PHE 157, /C LYS 187, /C GLY 261, /C TYR
449, /C ASN 460, /C ASN 487, /C VAL 503, /C ASN 641, /C VAL 687, /C ARG 815,
/C GLN 853  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A HIS 66, /A THR 95, /A
GLY 142, /A LEU 176, /A ARG 246, /A ARG 328, /A SER 443, /A ARG 454, /A THR
500, /A VAL 620, /A ALA 672, /A LYS 811, /A LEU 828, /A ASP 1146, /B HIS 66,
/B LEU 141, /B LEU 176, /B PRO 209, /B LEU 242, /B SER 443, /B ARG 454, /B TYR
473, /B THR 500, /B VAL 620, /B ALA 672, /B LYS 811, /B LEU 828, /B ASP 1146,
/C HIS 66, /C THR 95, /C PHE 140, /C LEU 176, /C HIS 245, /C SER 443, /C ARG
454, /C GLU 471, /C GLN 498, /C VAL 620, /C ALA 672, /C LYS 811, /C LEU 828,
/C ASP 1146  
2019 hydrogen bonds  
Adding 'H' to /A ALA 27  
Adding 'H' to /A PHE 79  
Adding 'H' to /A ASN 99  
Adding 'H' to /A GLU 156  
Adding 'H' to /A LYS 187  
35 messages similar to the above omitted  
/A HIS 66 is not terminus, removing H atom from 'C'  
/A THR 95 is not terminus, removing H atom from 'C'  
/A GLY 142 is not terminus, removing H atom from 'C'  
/A LEU 176 is not terminus, removing H atom from 'C'  
/A ARG 246 is not terminus, removing H atom from 'C'  
37 messages similar to the above omitted  
21811 hydrogens added  
  

> hide HC

> volume gaussian #1 bfactor 80

Missing or invalid "volumes" argument: invalid models specifier  

> clipper associate #2 toModel #1

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

> clipper spotlight radius 19.00

> select #1

44665 atoms, 45229 bonds, 39 pseudobonds, 16 models selected  

No template found for residue B709 (ASN)  

Doing nothing  

> toolshed show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select up

26 atoms, 26 bonds, 1 model selected  

> show sel

> select #1

44667 atoms, 45231 bonds, 39 pseudobonds, 22 models selected  

No template found for residue C282 (ASN)  

Doing nothing  




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

[Eric Pettersen]

Mmmm, not a fan of monkey-patching AddH for particular residue types / atom names. That road is really endless.

You know, you can actually get the protonation on that structure correct with "addh template true" followed by a second round of "addh"! The first pass gets the C1 correct but the N wrong (templates are not applied to modified residues). The second round reassesses the type of the N now that it knows that C1 is sp3 rather than sp2 and protonates the N.

I think what I can do is rework the "template true" code to apply the template types and then force a recomputation of non-explicitly assigned atoms. That might get it to work in one pass.

--Eric

[Tristan Croll]

That sounds promising!

— Tristan
 

 

[Eric Pettersen]

Fixed. Works in one pass now.