AlphaFold second prediction overwrites first prediction

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202108251821 (2021-08-25 18:21:58 UTC)
Description
Running a second AlphaFold prediction without closing the Colab window put the results in the same Downloads directory prediction_12 and loaded the wrong file for the second prediction since it was named best_model (2).pdb.

Log:
UCSF ChimeraX version: 1.3.dev202108251821 (2021-08-25)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7jtl

Summary of feedback from opening 7jtl fetched from pdb  
---  
note | Fetching compressed mmCIF 7jtl from
http://files.rcsb.org/download/7jtl.cif  
  
7jtl title:  
Structure of SARS-CoV-2 ORF8 accessory protein [more info...]  
  
Chain information for 7jtl #1  
---  
Chain | Description | UniProt  
A B | ORF8 protein | NS8_SARS2  
  
Non-standard residues in 7jtl #1  
---  
NA — sodium ion  
  

> ui tool show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

ChimeraX REST job id: job_3wikysds  
BlastProtein finished.  
Parsing BLAST results.  

> blastprotein /A database pdb cutoff 1e-1 matrix BLOSUM62 maxSeqs 100 name
> bp1

ChimeraX REST job id: job_1tomv5gm  
BlastProtein finished.  
Parsing BLAST results.  

> open pdb:7JX6

Summary of feedback from opening 7JX6 fetched from pdb  
---  
note | Fetching compressed mmCIF 7jx6 from
http://files.rcsb.org/download/7jx6.cif  
  
7jx6 title:  
STRUCTURE OF THE SARS-CoV-2 ORF8 ENCODED ACCESSORY PROTEIN [more info...]  
  
Chain information for 7jx6 #2  
---  
Chain | Description | UniProt  
A B | ORF8 protein | NS8_SARS2  
  
Non-standard residues in 7jx6 #2  
---  
NA — sodium ion  
  
7jx6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  

> matchmaker #2/B to #1/A

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 7jtl, chain A (#1) with 7jx6, chain B (#2), sequence alignment
score = 509.5  
RMSD between 82 pruned atom pairs is 0.471 angstroms; (across all 88 pairs:
1.033)  
  

> close

> open /Users/goddard/Desktop/rotavirus_nsp5.fasta

Summary of feedback from opening /Users/goddard/Desktop/rotavirus_nsp5.fasta  
---  
note | Alignment identifier is rotavirus_nsp5.fasta  
  
Opened 1 sequences from rotavirus_nsp5.fasta  

> ui dockable true "Sequence Viewer"

> blastprotein rotavirus_nsp5.fasta:1

ChimeraX REST job id: job_nt3nk849  
BlastProtein finished.  
Parsing BLAST results.  

> usage blastprotein

blastprotein atoms [database database] [cutoff a number] [matrix matrix]
[maxSeqs an integer] [log true or false] [name a text string]  
— Search PDB/NR using BLAST  
atoms: an atom specifier or [alignment-id:]sequence-name-or-number  
database: one of alphafold, nr, or pdb  
matrix: one of BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, IDENTITY,
PAM250, PAM30, or PAM70

blastprotein mav [name] [selected true or false]  
— Display BLAST results in MultAlign Viewer  
name: a text string  

> help blastprotein

> blastprotein rotavirus_nsp5.fasta:1 cutoff 1e-1

ChimeraX REST job id: job_ai_aq1xu  
BlastProtein finished.  
Parsing BLAST results.  

> ui tool show AlphaFold

> alphafold match
> MSLSIDVTSLPSIPSTIYKNESSSTTSTLSGKSIGRSEQYISPDAEAFNKYMLSKSPEDIGPSDSASNDPLTSFSIRSNAVKTNADAGVSMDSSAQSRPSSNVGCDQVDFSLNKGLKVKANLDSSISISTDTKKEKSKQNHKSRKHYPRIEAESDSDDYVLDDSDSDDGKCKNCKYKKKYFALRMRMKQVAMQLIEDL

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  

> alphafold search
> MSLSIDVTSLPSIPSTIYKNESSSTTSTLSGKSIGRSEQYISPDAEAFNKYMLSKSPEDIGPSDSASNDPLTSFSIRSNAVKTNADAGVSMDSSAQSRPSSNVGCDQVDFSLNKGLKVKANLDSSISISTDTKKEKSKQNHKSRKHYPRIEAESDSDDYVLDDSDSDDGKCKNCKYKKKYFALRMRMKQVAMQLIEDL

ChimeraX REST job id: job_og1yw3d6  
BlastProtein finished.  
Parsing BLAST results.  

> alphafold predict
> MSLSIDVTSLPSIPSTIYKNESSSTTSTLSGKSIGRSEQYISPDAEAFNKYMLSKSPEDIGPSDSASNDPLTSFSIRSNAVKTNADAGVSMDSSAQSRPSSNVGCDQVDFSLNKGLKVKANLDSSISISTDTKKEKSKQNHKSRKHYPRIEAESDSDDYVLDDSDSDDGKCKNCKYKKKYFALRMRMKQVAMQLIEDL

Running AlphaFold prediction  
Fetching A2T3S0 UniProt info from https://www.uniprot.org/uniprot/A2T3S0.xml  

> alphafold search RDRP_ROTSH

ChimeraX REST job id: job_g9n13bed  
BlastProtein finished.  
Parsing BLAST results.  
Fetching A2T3M4 UniProt info from https://www.uniprot.org/uniprot/A2T3M4.xml  

> alphafold search NSP1_ROTSH

ChimeraX REST job id: job_qv33bcre  
BlastProtein finished.  
Parsing BLAST results.  
AlphaFold prediction finished  
Results in /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_12  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> show atoms

> hide atoms

Fetching P06179 UniProt info from https://www.uniprot.org/uniprot/P06179.xml  

> alphafold match FLIC_SALTY

1 UniProt id does not have an AlphaFold database model: P06179 (UniProt
FLIC_SALTY)  

Fetching compressed AlphaFold P04949 from
https://alphafold.ebi.ac.uk/files/AF-P04949-F1-model_v1.cif  
1 AlphaFold model found using sequence similarity searches: P04949 (UniProt
FLIC_SALTY)  
Opened 1 AlphaFold model  

> hide #1 models

> open FLIC_SALTY fromDatabase uniprot

Summary of feedback from opening FLIC_SALTY fetched from uniprot  
---  
notes | UniProt identifier FLIC_SALTY maps to entry P06179  
Fetching FLIC_SALTY UniProt info from
https://www.uniprot.org/uniprot/FLIC_SALTY.xml  
Alignment identifier is FLIC_SALTY  
  
Opened UniProt FLIC_SALTY  

> sequence associate #2/A FLIC_SALTY:1

Associated UniProt P04949 chain A to FLIC_SALTY with 238 mismatches and/or
gaps  

> alphafold search FLIC_SALTY

ChimeraX REST job id: job_woy004sw  
BlastProtein finished.  
Parsing BLAST results.  

> alphafold fetch P04949

Chain information for AlphaFold P04949 #3  
---  
Chain | Description | UniProt  
A | Flagellin | FLIC_ECOLI  
  

> select clear

Fetching A2T3R0 UniProt info from https://www.uniprot.org/uniprot/A2T3R0.xml  

> alphafold predict NSP6_ROTSH

Running AlphaFold prediction  

> hide #3 models

> hide #2 models

> show #1 models

AlphaFold prediction finished  
Results in /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_12  
Chain information for best_model.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> open "/Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_12/best_model
> (2).pdb"

Chain information for best_model (2).pdb #5  
---  
Chain | Description  
A | No description available  
  




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[Tom Goddard]

Fixed.

AlphaFold Run tool was a single instance and remembered the download directory from the first run. Made it forget the directory once the results are downloaded and shown.