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Opened 4 years ago
Closed 4 years ago
#5287 closed defect (fixed)
Blast NR search omits the sequence hits
| Reported by: | Elaine Meng | Owned by: | Zach Pearson |
|---|---|---|---|
| Priority: | high | Milestone: | 1.3 |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Blast NR search with identical query and parameters gives plenty of sequence-only hits in Chimera, but they are omitted in ChimeraX! Sessions for Chimera and ChimeraX attached from running identical searches.
Attachments (3)
Change History (11)
by , 4 years ago
| Attachment: | nrblast.cxs added |
|---|
comment:1 by , 4 years ago
Hmm... It looks like this was probably the commit that broke this, but I'm not sure why at the moment.
Looking at the code from 1.2.5, it looked like we were only supposed to keep PDB hits, so the code was always designed to filter out non-PDB hits. If that's not what we want for NR, I can write another parser just for NR that will take all the hits.
comment:2 by , 4 years ago
Blast in 1.2.5 and earlier most definitely kept the sequence-only hits! Otherwise it would completely defeat the purpose of searching NR. I'll get you a 1.2.5 session with NR search results.
comment:3 by , 4 years ago
I'm definitely not disputing that we want the sequence-only hits, I agree, I'm only pointing out the confusing comment from 1.2.5 that led to that design choice -- we'll get those sequence only hits in, don't worry!
follow-up: 2 comment:4 by , 4 years ago
Maybe that comment referred to the structure-loading actions? But I really have no idea, as I didn't write it...
by , 4 years ago
| Attachment: | nrblast-125.cxs added |
|---|
session with results of same search in ChimeraX 1.2.5
comment:5 by , 4 years ago
I believe that comment means that it looks through the nr defline for PDB IDs that could be loaded for that nr hit, not that it tosses the nr hit.
follow-up: 4 comment:6 by , 4 years ago
See comment 5 and 6 of #5241 -- the first half of 5 and all of 6 applied here. Bookkeeping error on my end.
comment:7 by , 4 years ago
This commit should restore sequence only hits. Additionally the scaffolding is there to get the URL for #5241.
follow-up: 5 comment:8 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
ChimeraX session