Opened 5 months ago
Last modified 5 months ago
#17792 accepted defect
Edge case PDB file freezes ChimeraX
Reported by: | Roden Deng Luo | Owned by: | Eric Pettersen |
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Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
Hi, I downloaded the attached file from https://zenodo.org/records/14271435. Trying to open It just freezes ChimeraX version 1.9 (2024-12-11) on Ubuntu. In debug mode in PyCharm, I could not pause the program to see the potential problem. The major difference between it and the official 1KBH is that all the models/states are concatenated and there is no header or metadata. An error message would be good. Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
Attachments (3)
Change History (5)
by , 5 months ago
Attachment: | difference_summary.txt added |
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comment:1 by , 5 months ago
Component: | Unassigned → Input/Output |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Why would they "flatten" a file like this? It makes no sense. It saves a trivial amount of storage space relative to that taken by the coordinate records.
comment:2 by , 5 months ago
My guess is this may be some kind of "common" practice in the deep learning (DL) world for protein structures. I saw quite some single state cases (not causing any problems) as such before, from different DL projects. For this specific case, the direct ref, PPB-Affinity (https://www.nature.com/articles/s41597-024-03997-4) reported a curated dataset, potentially subject to DL uses. The previously attached specific data point originated from SKEMPI 2.0 https://academic.oup.com/bioinformatics/article/35/3/462/5055583. The paper has a "Processed PDB files" section. But it is not clear to me why those mentioned intentions would result in such an end file. I used the attached python script to detect multiple occurrences of chain-residue number pairs; if such, I delete the data point from my current pipeline. There are about 200 such cases in PPB-Affinity. On Tue, May 27, 2025 at 10:08 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > >
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