Opened 4 years ago

Closed 4 years ago

#5394 closed defect (fixed)

Blast Protein empty Ligand Symbols column

Reported by: Elaine Meng Owned by: Zach Pearson
Priority: high Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Seems like something went awry with parsing ligand symbols. E.g.
open 1hag
blast #1/e

...Ligand Symbols column is totally blank. At first I thought none of the structures had ligands, but then when I showed ligand names, ligand smiles, etc. For example, top hit 5EDM has NAG, SO4, GOL, etc. as listed on its page at the RCSB PDB. ​https://www.rcsb.org/structure/5EDM

Tested in daily build UCSF ChimeraX version: 1.3.dev202110120902 (2021-10-12)

Attachments (1)

Screen Shot 2021-10-12 at 12.08.41 PM.png​ (367.2 KB ) - added by Elaine Meng 4 years ago.
screenshot of Blast results showing blank Ligand Symbols column

Download all attachments as: .zip

Change History (5)

by Elaine Meng, 4 years ago

Attachment: Screen Shot 2021-10-12 at 12.08.41 PM.png​ added

screenshot of Blast results showing blank Ligand Symbols column

comment:1 by Zach Pearson, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in ​this commit.

in reply to:  3 comment:2 by Elaine Meng, 4 years ago 

Sorry, not fixed:  now the Ligand Symbols column shows the same thing as Ligand Formulas.  Ligand Symbols is supposed to be the residue names in the PDB file: MG, GOL, SO4, etc.

comment:3 by Elaine Meng, 4 years ago

Resolution: fixed
Status: closed → reopened

comment:4 by Zach Pearson, 4 years ago

Resolution: → fixed
Status: reopened → closed

I had the wrong graphql query, sorry! ​This definitely fixes it.

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