"combine" with blank chain ID

[Tony Schaefer]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.dev202306232350 (2023-06-23 23:50:16 UTC)
Description
I combined two structures (one from Gaussian output, one from iupac name) and then couldn't calculate the distances involving any atoms in the iupac structure. It looks like this might be because it doesn't have a valid chain id assigned, so the "?" in place of the chain id in the atomspec was matching multiple atoms. In the shell, I can see that the chain_id was a single space for the part of the structure that is from `open iupac:benzene`. Once I set the chain id to something else, I can calculate the distances. 

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> cd C:\Users\ajs99778/Desktop

Current working directory is: C:\Users\ajs99778\Desktop  

> graphics selection width 4

UCSF ChimeraX version: 1.7.dev202306232350 (2023-06-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\ajs99778\Desktop\ts-opt-freq.out format out

Summary of feedback from opening C:\Users\ajs99778\Desktop\ts-opt-freq.out  
---  
notes | coords 0  
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coords 14  
coords 15  
coords 16  
coords 17  
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coords 19  
21  
  
Opened ts-opt-freq.out as an ORCA output file  

> close

> open C:\Users\ajs99778\Desktop\ts-opt-freq.out format out

Summary of feedback from opening C:\Users\ajs99778\Desktop\ts-opt-freq.out  
---  
notes | coords 0  
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coords 14  
coords 15  
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coords 17  
coords 18  
coords 19  
21  
  
Opened ts-opt-freq.out as an ORCA output file  

> close

> open C:/Users/ajs99778/Downloads/c_o_21_free.log

Summary of feedback from opening C:/Users/ajs99778/Downloads/c_o_21_free.log  
---  
notes | c_o_21_free.log has 1 imaginary harmonic vibrational mode  
243.01i  
10  
  
Opened c_o_21_free.log as a Gaussian output file  

> ui tool show "Visualize Normal Modes"

> close

> open C:\Users\ajs99778\Desktop\ts-opt-freq.out format out

Summary of feedback from opening C:\Users\ajs99778\Desktop\ts-opt-freq.out  
---  
notes | coords 0  
coords 0  
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coords 11  
coords 12  
coords 13  
coords 14  
coords 15  
coords 16  
coords 17  
coords 18  
coords 19  
21  
  
Opened ts-opt-freq.out as an ORCA output file  

> ui tool show "File Info"

> close

> open C:\Users\ajs99778\Desktop\ts-opt-freq.out format out

Summary of feedback from opening C:\Users\ajs99778\Desktop\ts-opt-freq.out  
---  
notes | coords 0  
coords 0  
coords 1  
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coords 3  
coords 4  
coords 5  
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coords 11  
coords 12  
coords 13  
coords 14  
coords 15  
coords 16  
coords 17  
coords 18  
coords 19  
21  
  
Opened ts-opt-freq.out as an ORCA output file  

> close

> open C:\Users\ajs99778\Desktop\cat.log format log

Summary of feedback from opening C:\Users\ajs99778\Desktop\cat.log  
---  
notes | 51  
  
Opened cat.log as a Gaussian output file  

> open iupac:benzene

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Translated IUPAC name to SMILES string via Cambridge web service (IUPAC:
benzene)  
Translated SMILES to 3D structure via NCI web service (SMILES: C1=CC=CC=C1)  

> ui mousemode right "select fragment"

> ui mousemode right "translate selected atoms"

> combine #1 #2

> close #2#1

> preset seqcrow "ball-stick-endcap (displayed only)"

Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> ui tool show "Build QM Input"

> ui mousemode right distance

> distance /?:1@C1 /a:1@Mo1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects  

> distance /?:1@C1 /a:1@Mo1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects  

> distance /a:1@Mo1 /?:1@C1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects  

> distance /a:1@H8 /a:1@Mo1

Distance between /a UNK 1 H8 and Mo1: 3.57Å  

> distance /?:1@H6 /?:1@H1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 4 atoms and 0
measurable objects  

> select clear

> distance /?:1@C4 /?:1@C1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 4 atoms and 0
measurable objects  

> distance /a:1@H19 /?:1@H2

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects  

> distance /?:1@C1 /a:1@Mo1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects  

> open iupac:benzene

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Translated IUPAC name to SMILES string via Cambridge web service (IUPAC:
benzene)  
Translated SMILES to 3D structure via NCI web service (SMILES: C1=CC=CC=C1)  

> hide #!1 models

> show #!1 models

> hide #!3 models

> distance #2/?:1@C4 #2/?:1@C1

Distance between iupac:benzene #2/? UNL 1 C4 and C1: 2.76Å  

> hide #2 models

> show #!3 models

> distance #3/?:1@C4 #3/?:1@C1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 4 atoms and 0
measurable objects  

> show #2 models

> hide #1.1 models

> show #1.1 models

> hide #!3 models

> show #!3 models

> hide #1.1 models

> hide #2 models

> show #1.1 models

Drag select of 12 atoms, 12 bonds  

> help setattr

> setattr sel chains name b

Assigning name attribute to 0 items  

> ui tool show Shell

0.01s - Debugger warning: It seems that frozen modules are being used, which
may  
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off  
0.00s - to python to disable frozen modules.  
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.  

> setattr sel chains id b

Assigning id attribute to 0 items  

> setattr sel res chain_id b

Assigning chain_id attribute to 1 item  

> distance #3/a:1@Mo1 #3/b:1@C1

Distance between combination #3/a UNK 1 Mo1 and /b UNL 1 C1: 6.80Å  

> show #2 models

> hide #!3 models

> help combine

> show #!3 models

> hide #2 models

> ui mousemode right "translate selected atoms"




OpenGL version: 3.3.0 - Build 31.0.101.4953
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7000
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 16,853,479,424
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
OSLanguage: en-US

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[Eric Pettersen]

Hi Tony,

As you discovered, ChimeraX atom specifiers cannot handle a model that has both blank and non-blank chain IDs. The "combine" command in the daily build no longer allows that -- it remaps the blank chain ID to an available non-blank ID.

--Eric