Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6001 closed defect (fixed)

Problems specifying AlphaFold arguments

Reported by: martti.tolvanen@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc: pett, Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
The bug I reported a bit earlier, while starting ChimeraX for the first time, did not repeat in starting it again.

Current problem: I cannot start alphafold multimer predictions. I wonder if the reason is that in my Windows locale comma is a decimal separator? In the log you see that many instances where the sequence or chain identifier works for a single protein but not when trying to do a dimer of that chain. I did try with a space after the comma as well until I read that no spaces are allowed...

Related problem: If I choose a sequence in the multalign viewer which has gaps, Alphafold stops telling me there are illegal characters, periods. I didn't find a setting for changing the gap character into a dash. Does that setting exist in ChimeraX?

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7262 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open P23280

Unknown command: alphafold open P23280  

> alphafold fetch P23280

Fetching compressed AlphaFold P23280 from
https://alphafold.ebi.ac.uk/files/AF-P23280-F1-model_v1.cif  
Chain information for AlphaFold P23280 #1  
---  
Chain | Description | UniProt  
A | Carbonic anhydrase 6 | CAH6_HUMAN  
  
Alignment identifier is 1/A  

> select /A:18

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

> select /A:18

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

> delete :1-17

> alphafold predict /A,/A

Missing or invalid "sequence" argument: Sequences argument "/A,/A" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict /A, /A

Missing or invalid "sequence" argument: Sequences argument "/A," is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict A, A

Missing or invalid "sequence" argument: Sequences argument "A," is not a chain
specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict #1/A, #1/A

Missing or invalid "sequence" argument: Sequences argument "#1/A," is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict 1/A, 1/A

Missing or invalid "sequence" argument: Sequences argument "1/A," is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict "chain A", "chain A"

Missing or invalid "sequence" argument: Sequences argument "chain A", "chain
A" is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold fetch P23280

Chain information for AlphaFold P23280 #2  
---  
Chain | Description | UniProt  
A | Carbonic anhydrase 6 | CAH6_HUMAN  
  

> delete :1-17

> ui tool show "Show Sequence Viewer"

> alphafold predict AlphaFold P23280 #1/A, AlphaFold P23280 #2/A

Missing or invalid "sequence" argument: Sequences argument "AlphaFold" is not
a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict #1/A,#2/A

Missing or invalid "sequence" argument: Sequences argument "#1/A,#2/A" is not
a chain specifier, alignment id, UniProt id, or sequence characters  

> select
> #1/A:51-52,58-59,67-69,74-82,87-90,96-98,104-114,127-128,131-132,135-143,159-169,193-199,212-217,228-240,252,258,275-276

733 atoms, 738 bonds, 88 residues, 1 model selected  

> select #1/A:18

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

> select #1/A:18

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

> select #1/A:18-248

1852 atoms, 1908 bonds, 231 residues, 1 model selected  

> sequence chain #1/A #2/A

Alignment identifier is 1  

> select #1/A:308 #2/A:308

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1/A:121-308 #2/A:121-308

3130 atoms, 3218 bonds, 376 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [121-308] RMSD: 0.000  
  

> select #1/A:121-308 #2/A:121-308

3130 atoms, 3218 bonds, 376 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [121-308] RMSD: 0.000  
  

> select #1/A:18 #2/A:18

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1/A:18-180 #2/A:18-180

2582 atoms, 2658 bonds, 326 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [18-180] RMSD: 0.000  
  

> select #1/A:178 #2/A:178

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:178-300 #2/A:178-300

2072 atoms, 2132 bonds, 246 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [178-300] RMSD: 0.000  
  

> ui tool show AlphaFold

> alphafold predict #1

Running AlphaFold prediction  
[Repeated 3 time(s)]

> select #1/A:20 #2/A:20

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1/A:18-20 #2/A:18-20

52 atoms, 52 bonds, 6 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [15-20] RMSD: 0.000  
  

> alphafold predict
> "QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN","QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN","QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> "QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN","QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN","QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> "QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN",
> "QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN",
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> "QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN","QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN","QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> ui tool show Matchmaker

> matchmaker #2 to #1

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 AlphaFold P23280, chain A (#1) with AlphaFold P23280, chain A (#2),
sequence alignment score = 1590.1  
RMSD between 291 pruned atom pairs is 0.000 angstroms; (across all 291 pairs:
0.000)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1 showAlignment true

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 AlphaFold P23280, chain A (#1) with AlphaFold P23280, chain A (#2),
sequence alignment score = 1590.1  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: AlphaFold P23280 #1/A,
AlphaFold P23280 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 291 pruned atom pairs is 0.000 angstroms; (across all 291 pairs:
0.000)  
  

> select

4748 atoms, 4886 bonds, 582 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2 to #1 showAlignment true

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 AlphaFold P23280, chain A (#1) with AlphaFold P23280, chain A (#2),
sequence alignment score = 1590.1  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: AlphaFold P23280 #1/A,
AlphaFold P23280 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 291 pruned atom pairs is 0.000 angstroms; (across all 291 pairs:
0.000)  
  

> save C:/Users/meetol/Desktop/af-ca6-two.fasta format fasta alignment 1

> ui tool show AlphaFold

> help help:user/tools/alphafold.html

> open C:/Users/meetol/Desktop/af-ca6-two.fasta

Summary of feedback from opening C:/Users/meetol/Desktop/af-ca6-two.fasta  
---  
notes | Alignment identifier is af-ca6-two.fasta  
Associated AlphaFold P23280 chain A to AlphaFold P23280, chain A with 0
mismatches  
Associated AlphaFold P23280 chain A to AlphaFold P23280, chain A with 0
mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment af-ca6-two.fasta  
  
Opened 2 sequences from af-ca6-two.fasta  

> alphafold predict af-ca6-two.fasta:1,af-ca6-two.fasta:2

Missing or invalid "sequence" argument: Sequences argument "af-
ca6-two.fasta:1,af-ca6-two.fasta:2" is not a chain specifier, alignment id,
UniProt id, or sequence characters  

> alphafold predict 1,2

Missing or invalid "sequence" argument: Sequences argument "1,2" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

Missing or invalid "sequence" argument: Sequences argument
"QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN,QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

Running AlphaFold prediction  
Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in C:\Users\meetol/Downloads\ChimeraX\AlphaFold\prediction_1  

> close #2

> ui tool show Matchmaker

> matchmaker #3 to #1 showAlignment true

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 AlphaFold P23280, chain A (#1) with best_model.pdb, chain A (#3),
sequence alignment score = 1518.2  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: AlphaFold P23280 #1/A,
best_model.pdb #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 271 pruned atom pairs is 0.333 angstroms; (across all 291 pairs:
1.011)  
  

> alphafold predict 2,2

Missing or invalid "sequence" argument: Sequences argument "2,2" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict 2,2

Missing or invalid "sequence" argument: Sequences argument "2,2" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict 2,2

Missing or invalid "sequence" argument: Sequences argument "2,2" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict 2

Running AlphaFold prediction  

> 2dlabels

> alphafold predict
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

>
> QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN

Unknown command:
QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQFYLHKIEEILDYLRRALN  
Running AlphaFold prediction  
Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated best_model.pdb chain A to best_model.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: AlphaFold P23280 #1/A,
best_model.pdb #2/A, best_model.pdb #3/A  
AlphaFold prediction finished  
Results in C:\Users\meetol/Downloads\ChimeraX\AlphaFold\prediction_2  

> ui tool show Matchmaker

> matchmaker #3 to #2 showAlignment true

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 best_model.pdb, chain A (#2) with best_model.pdb, chain A (#3),
sequence alignment score = 1533.2  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #2/A,
best_model.pdb #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 291 pruned atom pairs is 0.000 angstroms; (across all 291 pairs:
0.000)  
  

> alphafold predict 2;2

Missing or invalid "sequence" argument: Sequences argument "2" is not a chain
specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict 2

Running AlphaFold prediction  

> 2dlabels

Chain information for best_model.pdb #4  
---  
Chain | Description  
A | No description available  
  
Associated best_model.pdb chain A to best_model.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #2/A,
best_model.pdb #3/A, best_model.pdb #4/A  
AlphaFold prediction finished  
Results in C:\Users\meetol/Downloads\ChimeraX\AlphaFold\prediction_3  

> alphafold predict 2,2

Missing or invalid "sequence" argument: Sequences argument "2,2" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict 2\,2

Missing or invalid "sequence" argument: Sequences argument "2\,2" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict 2\;2

Missing or invalid "sequence" argument: Sequences argument "2\" is not a chain
specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict #3/A

Running AlphaFold prediction  

> alphafold predict #3/A,#3/A

Missing or invalid "sequence" argument: Sequences argument "#3/A,#3/A" is not
a chain specifier, alignment id, UniProt id, or sequence characters  




OpenGL version: 3.3.0 - Build 26.20.100.7262
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 840 G3
OS: Microsoft Windows 10 Enterprise (Build 17763)
Memory: 8,464,723,968
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz
OSLanguage: en-US
Locale: ('fi_FI', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
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    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
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    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-IMOD: 1.0
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    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
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Change History (11)

comment:1 by pett, 4 years ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problems specifying AlphaFold arguments

comment:2 by Tom Goddard, 4 years ago

Cc: Tom Goddard added
Owner: changed from Tom Goddard to pett

ChimeraX 1.3 does not support AlphaFold multimer prediction. That was added to ChimeraX after the 1.3 release and is in the ChimeraX 1.4 daily builds.

I don't know the answer to your question about changing the gap character in sequence viewer from "." to "-" but Eric Pettersen can advise on that.

comment:3 by pett, 4 years ago

Cc: pett added; Tom Goddard removed
Owner: changed from pett to Tom Goddard

If AlphaFold does not handle gap characters, then it should be passed seq.ungapped().characters rather than seq.characters

comment:4 by Tom Goddard, 4 years ago

Cc: Elaine Meng added

Looking at your Log I see you tried many creating attempts to run alphafold predicting a homodimer. Of course they were all doomed to fail because ChimeraX version 1.3 does not predict multimers. But most of your command syntax tries for "alphafold predict" also won't work in ChimeraX daily builds which does predict multimers. Here is an explanation of commands that won't work and an explanation why.

"alphafold predict /A,/A". This looks very reasonable like it should predict for a homodimer of chain A. Sadly it won't work for two reasons. First /A,/A is does not follow ChimeraX atom specifier syntax (you can try "select /A,/A" and see it will give an error). You cannot have a command there. You can say /A,A or /A,B or /A /A (with or without a space) but none of those are going to do what you want because they only give one copy of chain A. The ChimeraX atom specifications do not offer a way to specify two copies of the same atoms.

"alphafold predict #1/A, #1/A" Same problem as the previous example.

The alphafold predict command can take a single atom specifier. It cannot take two atom specifiers separated by commas, because he atom specifiers themselves contain commas and the code is not smart enough to figure out which comma separates different specifiers versus commas within a specifier.

"alphafold predict af-ca6-two.fasta:1,af-ca6-two.fasta:2" This should work in ChimeraX 1.4 daily bulids, specifying sequence viewer sequences.

"alphafold predict QHVSDWTYS...,QHVSDWTYS..." This will work in ChimeraX 1.4.

"alphafold predict #1/A,#2/A" Again an illegal atom specifiers but "#1,​2/A" or "#1/A#2/A" or "#1/A #2/A" or just "/A" would work and this does get you two copies of the same chain since they are different sets of atoms.

I'll see if we can improve the documentation to make clear that "atom-spec,atom-spec" will not work.

in reply to:  5 ; comment:5 by Elaine Meng, 4 years ago 

The documentation already does say that the multiple chains can be specified *either* collectively with a chain-spec (where "chain-spec" is a link to command-line atomspec documentation) *or* as a comma-separated list of other types of specification (sequence ID in viewer, uniprot ID, raw sequence).  

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#predict>

It doesn't have the asterisks, however, that I included here for emphasis.

Maybe I can do one or more of the following
(1) bold-italicize "either" and "or"
(2) say that you cannot use the chain-spec method to specify more copies than are already in the currently open structure; instead you have to actually open multiple copies beforehand or use one of the other specification methods
(3) I know you (TG) always want examples but they are not as useful when the dominant factor as to what will happen is what structures the person has open at the time.  Will think about having examples that explicitly also say what is open, but I didn't want to make the documentation a worse "wall of text" than it is already.

in reply to:  6 ; comment:6 by goddard@…, 4 years ago 

Actually I think Martti's try

	alphafold predict /A,/A

seem the most reasonable and I can make that work in a way I think is reasonable.  First the command will try to interpret that as a single atom specifier which will fail because syntax is illegal.  Then it will try splitting it at commas and interpreting each part as an atom specifier and in this case that will work.  Some more complicated cases won't work, like  "#1/A,B,#2/C" because here the commas are both used within one specifier (#1/A,B) and between the specifiers #1/A,B", "#2/C".  But that is an exotic rare case and it will produce an error saying it could not be interpreted.  The only case the new use of commas really helps with is when you want to use more than one copy of the same chain.  In all other cases you can just specify a single legal atom spec, like "#1/A,B #2/C".

comment:7 by Tom Goddard, 4 years ago

Ok, I changed the code to allow comma-separated atom specifiers. First it tries to interpret as a single atom specifier and if that is not legal syntax then it splits it at commas and tries to interpret each as a single chain atom specifier. It will not accept #1,#2 if either models 1 and 2 have more than one chain, that case should use #1,​2 (single atom specifier).

comment:8 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed the other problem you asked about "." gap characters when using a multiple sequence alignment sequence in the alphafold prediction command, like

alphafold predict 1:2

where 1 is the alignment identifier and this specifies to use the second sequence of the alignment. The code now removes the gap characters since AlphaFold does not handle those. Or maybe AlphaFold does handle a gap, but the Google Colab script ChimeraX uses to handle gaps does not allow that.

in reply to:  9 ; comment:9 by martti.tolvanen@…, 4 years ago 

Thank you very much for the exhaustive comments. Obviously the major cause
of my problem was to view documentation directly from ChimeraX web site
without realizing it was for another version. So I'll try my luck with the
multimer predictions tomorrow. I should be able to get the syntax right by
Tom's advice.

Regarding documentation, I found the page of sequencespec rather unhelpful.

A related question: is there any way to destroy sequence from an existing
model? Just deleting atoms will leave the sequence there (enclosed in a red
rectangle) so my goal of creating a model of the mature protein, omitting
residues 1-17 of my target protein, seemed possible only with the literal
sequence string syntax. I can envision this happening by editing a pdb file
manually, but is there any way to do that in ChimeraX?

Cheers,
-Martti



ma 24. tammik. 2022 klo 23.09 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
kirjoitti:

in reply to:  10 ; comment:10 by Elaine Meng, 4 years ago 

If you mean this page,
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/seqspec.html>
...it applies only to the case of sequences already being shown in the Sequence Viewer.  Was that unclear?  It includes an example, and I'm not sure how to make it any clearer.   If you can clarify what exactly is unhelpful maybe I can make it better.

That page is referenced by multiple commands that can use that type of specification.  For modularity of documentation, it does not include the other methods (uniprot ID, raw sequence text) that only the alphafold command can use currently.

As to your question:
Showing the sequence from a structure uses the complete sequence record from the file, e.g. the SEQRES records in a PDB file and the logical equivalent in an mmCIF. It does not use the coordinates unless those other types of sequence information are missing.  Thus it makes no difference if you deleted part of the structure, unless you also edited the file to remove the SEQRES records before opening it.

The only other way I can think of is to put your modified sequence in some sequence-format file like fasta, then open it so that it's shown in the Sequence Viewer, and then use sequence-spec as mentioned above.  E.g. if your file is named blah.fa, then the sequence-spec would be 

blah.fa:1

Here are the sequence formats ChimeraX knows:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#sequence>

Elaine

comment:11 by Tom Goddard, 4 years ago

Hi Martii,

Specifying sequences in commands in a variety of ways (uniprot id, chain specifier, explicit sequence) is new, added for the alphafold command. I like the improvement this bug report inspired of a way to specify a homo-dimer as /A,/A just what you tried so that is in the daily builds now. Specifying a subsequence is also an interesting case. You want to /A:18-500 to omit the first 17 residues. But that won't work currently because specifying any atoms of chain A currently means all of chain A including parts of the sequence that don't even have atom coordinates. I don't think I can make that syntax work because the sequence for an experimental structure often includes residues that have no coordinates in the structure. I want you to be able to use that full sequence. The atom specifiers in ChimeraX only refer to atoms with coordinates -- the code gets a list of atoms that have coordinates, so specifiers can't list residue that have no coordinates.

Your attempt by deleting residues 1-17 was a good try. But ChimeraX does not forget the real sequence of the experimental sample -- various tools want to know the real full sequence. We could conceivably have some other command that says forget about the sequence for residues 1-17. You would probably never discover that command, it is such an obscure case.

So it looks to me like having the power to specify a subsequence with some command syntax is a bit too complicated. And of course there is a trivial way to get what you want now which is to paste the explicit sequence with the first 17 residues removed. I know, not the most convenient, but ChimeraX is primarily a 3D structure program so its sequence capabilities are not all powerful.

It would be good for us to mention in the documentation this case of trying to specify a subsequence and say that the only way is to paste an explicit sequence.

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