Cannot display missing structure

[shiysh6@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7rc202311230013 (2023-11-23 00:13:42 UTC)
Description
Can't display "the missing structure" when I input this pdb file 

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7rc202311230013 (2023-11-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open SenA fromDatabase pdb format mmcif

Fetching url http://files.rcsb.org/download/sena.cif failed:  
HTTP Error 404: Not Found  

> open F:/Desktop/SenA/8k5i.pdb

8k5i.pdb title:  
The structure of sena In complex with N,N,N-trimethyl-histidine and
thioglucose [more info...]  
  
Chain information for 8k5i.pdb #1  
---  
Chain | Description  
A | selenoneine synthase sena  
  
Non-standard residues in 8k5i.pdb #1  
---  
AVJ — N,N,N-trimethyl-histidine (hercynine)  
FE — Fe (III) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
GS1 — 1-thio-β-D-glucopyranose (1-thio-β-D-glucose; 1-thio-D-glucose; 1-thio-
glucose)  
PEG — di(hydroxyethyl)ether  
  

> log metadata #1

Metadata for 8k5i.pdb #1  
---  
Title | The structure of sena In complex with N,N,N-trimethyl-histidine and
thioglucose  
Citation | Structural insights INTO A novel nonheme iron-dependentoxygenase In
selenoneine biosynthesis. PMID: 38013086  
Non-standard residues | AVJ — N,N,N-trimethyl-histidine (hercynine)  
FE — Fe (III) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
GS1 — 1-thio-β-D-glucopyranose (1-thio-β-D-glucose; 1-thio-D-glucose; 1-thio-
glucose)  
PEG — di(hydroxyethyl)ether  
Gene source | Variovorax paradoxus  
Experimental method | X-ray diffraction  
Resolution | 1.92Å  
  
> hide #1.2 models

> show #1.2 models

> select subtract #1.2

Nothing selected  

> select add #1.2

Nothing selected  

> color #1.2 #ffaa7fff models




OpenGL version: 3.3.0 - Build 31.0.101.4502
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp65001
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 7400
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 16,889,192,448
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US

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File attachment: 8k5i.pdb

8k5i.pdb​

[shiysh6@…]

Added by email2trac

[Eric Pettersen]

Hi Yusheng,

I'm not sure what you mean when you say you can't display the missing structure. "Missing structure" is exactly what it says -- the 3D position of that part of the structure could not be determined by the experiment. ChimeraX depicts that with dashed lines between the parts that could be determined.
If you mean you want to know the sequence that's missing, you could click on "selenoneine synthase sena" in the log to show the full sequence, including the missing structure sequence.
If you mean you want ChimeraX to fill in the missing structure with estimated positions, you could use Tools→Structure Prediction→Model Loops or Tools→Structure Prediction→AlphaFold to do that.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab