AddH facing protons wrong

[Eric Pettersen]

The following bug report has been submitted:
Platform:        macOS-12.6.2-arm64-arm-64bit
ChimeraX Version: 1.7.dev202304150031 (2023-04-15 00:31:54 UTC)
Description
AddH is facing lone pairs towards negative moieties rather than facing protons (e.g. :183@oh, :573@o)

Log:
UCSF ChimeraX version: 1.7.dev202304150031 (2023-04-15)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/pett/rm/test.cxs format session

Log from Mon Apr 17 13:15:33 2023UCSF ChimeraX version: 1.7.dev202304150031
(2023-04-15)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6urx

Summary of feedback from opening 6urx fetched from pdb  
---  
notes | Fetching compressed mmCIF 6urx from
http://files.rcsb.org/download/6urx.cif  
Fetching CCD JMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/JMG/JMG.cif  
  
6urx title:  
Crystal structure of ricin A chain in complex with inhibitor
5-phenyl-2-thiophenecarboxylic acid [more info...]  
  
Chain information for 6urx #1  
---  
Chain | Description | UniProt  
A | Ricin | RICI_RICCO 1-267  
  
Non-standard residues in 6urx #1  
---  
DMS — dimethyl sulfoxide  
EDO — 1,2-ethanediol (ethylene glycol)  
JMG — 5-phenylthiophene-2-carboxylic acid  
  

> help split

> split ligands

Split 6urx (#1) into 18 models  
Chain information for 6urx #1.1  
---  
Chain | Description  
A | No description available  
  

> rename #1.2 id #2

> help hbonds

> hbonds intra f

Expected keyword "intraModel", "intraMol", or "intraRes"  

> hbonds intram f

Expected keyword "intraModel" or "intraMol"  

> hbonds intraModel false

7 hydrogen bonds found  

> help 2d

> 2dlabels text "Blue Fluorescent Protein" color light sea green size 26 xpos
> .03 ypos .92

> save /Users/pett/rm/test.cxs

——— End of log from Mon Apr 17 13:15:33 2023 ———

opened ChimeraX session  

> select #2/A:316@C14

1 atom, 1 residue, 1 model selected  

> select up

14 atoms, 15 bonds, 1 residue, 1 model selected  

> foc sel

Unknown command: foc sel  

> foc selview sel

Unknown command: foc selview sel  

> view sel

> label sel atoms attribute idatm_type

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warning | Not adding hydrogens to 6urx #1.1/A LYS 4 CB because it is missing
heavy-atom bond partners  
notes | No usable SEQRES records for 6urx (#1.1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 6urx #1.1/A LYS 4  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 6urx #1.1/A PRO 262  
711 hydrogen bonds  
6urx #1.1/A PRO 262 is not terminus, removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
2509 hydrogens added  
  

> hbonds

511 hydrogen bonds found  

> delete H

> hbonds

713 hydrogen bonds found  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warning | Not adding hydrogens to 6urx #1.1/A LYS 4 CB because it is missing
heavy-atom bond partners  
notes | No usable SEQRES records for 6urx (#1.1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 6urx #1.1/A LYS 4  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 6urx #1.1/A PRO 262  
710 hydrogen bonds  
6urx #1.1/A PRO 262 is not terminus, removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
2509 hydrogens added  
  

> save /Users/pett/rm/bug.cxs

> select :183@oh

1 atom, 1 residue, 1 model selected  

> select :573

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select :573@o

1 atom, 1 residue, 1 model selected  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac13,1
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.2 (21G320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 52 days 22:22

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        PHL 279P1:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
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    appdirs: 1.4.4
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    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
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    ChimeraX-AlignmentMatrices: 2.1
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File attachment: bug.cxs

bug.cxs​

[Eric Pettersen]

Added by email2trac

[Eric Pettersen]

One was not reproducible and the other was facing toward a closer acceptor (hidden by backbone ribbon)