UniProt sequences should retain numbering

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-6.8.0-59-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
If I:
- have a model (e.g. an AlphaFold structure) open containing a fragment of a larger protein
- open the associated UniProt entry
- renumber the protein residues to match the UniProt numbering:

"renumber /A start 647"

... then the protein model is renumbered correctly, but the complete associated sequence is renumbered to start from 647 (so residue 647 of the protein is now 1284 of the sequence).

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
Running command "isolde shorthand"  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Running command "open
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"  

> open perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
Running command "open
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb"  

> open perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Running command "open
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_3_seed_000.pdb"  

> open perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_3_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 1 time(s)]

> matchmaker #2,3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb, chain
B (#1) with
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb, chain
B (#2), sequence alignment score = 1288.8  
RMSD between 241 pruned atom pairs is 0.278 angstroms; (across all 247 pairs:
0.761)  
  
Matchmaker
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb, chain
B (#1) with
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_3_seed_000.pdb, chain
B (#3), sequence alignment score = 1288.8  
RMSD between 243 pruned atom pairs is 0.455 angstroms; (across all 247 pairs:
0.593)  
  

> cbc

Running command "ui tool show "AlphaFold Error Plot""  

> ui tool show "AlphaFold Error Plot"

Running command "alphafold pae #3 file
/home/tcroll/colabfold/predictions/perk_short_loop_tmem33/output/perk_loop_tmem33_scores_alphafold2_multimer_v3_model_3_seed_000.json"  

> alphafold pae #3 file
> /home/tcroll/colabfold/predictions/perk_short_loop_tmem33/output/perk_loop_tmem33_scores_alphafold2_multimer_v3_model_3_seed_000.json

> alphafold contacts #3/A toAtoms #3/B

Found 23 residue or atom pairs within distance 3  
Running command "hide #2 models"  

> hide #2 models

Running command "hide #1 models"  

> hide #1 models

> show #3

Running command "show #2 models"  

> show #2 models

Running command "show #1 models"  

> show #1 models

Running command "hide #!3 models"  

> hide #!3 models

Running command "hide #2 models"  

> hide #2 models

Running command "ui tool show "AlphaFold Error Plot""  

> ui tool show "AlphaFold Error Plot"

Running command "alphafold pae #1 file
/home/tcroll/colabfold/predictions/perk_short_loop_tmem33/output/perk_loop_tmem33_scores_alphafold2_multimer_v3_model_1_seed_000.json"  

> alphafold pae #1 file
> /home/tcroll/colabfold/predictions/perk_short_loop_tmem33/output/perk_loop_tmem33_scores_alphafold2_multimer_v3_model_1_seed_000.json

> alphafold contacts #1/B toAtoms #1/A

Found 15 residue or atom pairs within distance 3  

> show #1

> clipper init

Running command "cofr center showPivot t"  

> cofr centerOfView showPivot true

Running command "camera ortho"  

> camera ortho

Running command "lighting simple"  

> lighting simple

> renumber /A start 647

150 residues renumbered  

> open Q9NZJ5 fromDatabase uniprot

Summary of feedback from opening Q9NZJ5 fetched from uniprot  
---  
notes | Alignment identifier is Q9NZJ5  
Associated
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb chain A
to Q9NZJ5 with 0 mismatches  
Associated
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb chain A
to Q9NZJ5 with 0 mismatches  
Associated
perk_loop_tmem33_unrelaxed_alphafold2_multimer_v3_model_3_seed_000.pdb chain A
to Q9NZJ5 with 0 mismatches  
  
Opened UniProt Q9NZJ5  

> select /A:THR

21 atoms, 18 bonds, 3 residues, 3 models selected  
Running command "~sel"  

> ~select

Nothing selected  
Running command "wait 1"  
Running command "~sel"  

> ~select

Nothing selected  
Running command "wait 1"  
Running command "~sel"  

> ~select

Nothing selected  
Running command "wait 1"  
Running command "~sel"  

> ~select

Nothing selected  
Running command "wait 1"  
Running command "~sel"  

> ~select

Nothing selected  
Running command "wait 1"  

> close

Running command "open
/home/tcroll/colabfold/predictions/perk_short_loop_tmem33/output/perk_loop_tmem33_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"  

> open
> /home/tcroll/colabfold/predictions/perk_short_loop_tmem33/output/perk_loop_tmem33_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
perk_loop_tmem33_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Associated
perk_loop_tmem33_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
chain A to Q9NZJ5 with 0 mismatches  
Computing secondary structure  

> cbc

> renumber /A&protein start 647

50 residues renumbered  

> select /A

414 atoms, 431 bonds, 50 residues, 1 model selected  

> renumber /A start 1

50 residues renumbered  

> renumber /A start 647

50 residues renumbered  




OpenGL version: 3.3.0 NVIDIA 535.230.02
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        12Gi       7.2Gi       788Mi        11Gi        17Gi
	Swap:          2.0Gi       1.5Gi       487Mi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]	
	Kernel driver in use: nvidia

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