Found H-bonds differ

[Qchao.sun@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202203160044 (2022-03-16 00:44:37 UTC)
Description
"Tool-structure editing-Hbond", could not return any H bonds. While the H-bonds in "Molecule Display-H bonds" could give the right H bonds. 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.4.dev202203160044 (2022-03-16)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Qchao/Downloads/Bioluminescence/RLuc_CTZ.pdb

RLuc_CTZ.pdb title:  
Crystal structures of the luciferase and green fluorescent protein from
renilla reniformis [more info...]  
  
Chain information for RLuc_CTZ.pdb #1  
---  
Chain | Description | UniProt  
A B | renilla-TYPE luciferase | LUCI_RENRE  
  
Non-standard residues in RLuc_CTZ.pdb #1  
---  
CEI —
N-[3-benzyl-5-(4-hydroxyphenyl)pyrazin-2-yl]-2-(4-hydroxyphenyl)acetamide
(coelenteramide)  
  

> ui tool show H-Bonds

> select /A:290

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

45 atoms, 45 bonds, 5 residues, 1 model selected  

> select up

1274 atoms, 1305 bonds, 156 residues, 1 model selected  

> select up

1326 atoms, 1356 bonds, 163 residues, 1 model selected  

> select up

2503 atoms, 2572 bonds, 306 residues, 1 model selected  

> select up

2762 atoms, 2606 bonds, 535 residues, 1 model selected  

> select up

5521 atoms, 5212 bonds, 1067 residues, 1 model selected  

> select down

2762 atoms, 2606 bonds, 535 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /B:502@C11

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 34 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 showDist true interModel false intraModel false distSlop
> 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true
> reveal true retainCurrent true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> hbonds reveal true

897 hydrogen bonds found  

> select /B:502@C11

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 34 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 showDist true interModel false intraModel false distSlop
> 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true
> reveal true retainCurrent true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl  
Downloading bundle
/Users/Qchao/Downloads/ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl  
[Repeated 4 time(s)]

> ~hbonds

> addh

Summary of feedback from adding hydrogens to RLuc_CTZ.pdb #1  
---  
notes | No usable SEQRES records for RLuc_CTZ.pdb (#1) chain B; guessing
termini instead  
Chain-initial residues that are actual N termini: /B SER 3  
Chain-initial residues that are not actual N termini: /B GLU 155  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /B GLU 310, /B SER 152  
898 hydrogen bonds  
Adding 'H' to /B GLU 155  
/B GLU 310 is not terminus, removing H atom from 'C'  
2950 hydrogens added  
  

> select /B:502@C11

1 atom, 1 residue, 1 model selected  

> select up

52 atoms, 55 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 showDist true interModel false intraModel false distSlop
> 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true
> reveal true retainCurrent true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

52 atoms, 55 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

2 hydrogen bonds found  

> hbonds sel dashes 6 showDist true interModel false intraModel false distSlop
> 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true
> reveal true retainCurrent true

0 hydrogen bonds found  
0 strict hydrogen bonds found  
Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl  
[Repeated 1 time(s)]Downloading bundle
/Users/Qchao/Downloads/ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl  




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

Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 1 day 8:38

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL SE2419H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


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[Eric Pettersen]

Hi,

It looks like that when you used the tool you unchecked the "Include intermodal/intramodel/intramolecule/intraresidue" buttons. That means it will not find hydrogen bonds between models nor within models (the first two check buttons). It will also not find hydrogen bonds within the same bonded set of atoms or within the same residue, but that is superfluous because by unchecking those first two buttons you have prevented it from finding any H-bonds at all.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab