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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Getting PDB data stalls for hours and uses high GPU? #457

Closed orsburn closed 3 years ago

orsburn commented 3 years ago

Howdy CompOmics! I'm having trouble generating a 3D image of any proteins in PeptideShaker 2.0.25 and I also tried 2.0.6. just to see if it was a version issue. My 1080TI GPU went to "very high power usage" according to Windows 10 Pro (64-bit) and appeared to stay there for about 6 hours but it never generated an image. I also pulled the demo data and tried to make a 3D model of one of the HeLa proteins to no avail. I'm not sure where it's getting stuck, trying to pull down PDB data or actually modeling it. I'm allowing 32GB of RAM in Java 1.8 64-bit. Any ideas would be appreciated!

hbarsnes commented 3 years ago

Thanks for letting us know! It seems like the PDB web service has been reimplemented and the old one that PeptideShaker uses is no longer available. We will attempt to update to the new version, but I'm afraid we cannot guarantee that we will get the time to look at it in the near future.

You do not have to wait until the "Getting PDB data" dialog closes though (which it never will...), as you can simply close the dialog and the rest of the tool should work normally.

orsburn commented 3 years ago

Thanks for checking it out! I was able to install the PDB that I needed locally, but it doesn't have quite the same power. I'll watch out for the fix.

hbarsnes commented 3 years ago

I will let you know when it is working again. I will keep the issue open so that we do not forget about it.

hbarsnes commented 3 years ago

We've just released PeptideShaker v2.0.27 which should restore the PDB connection (by changing the web service used). Please let us know if this is not the case, and we'll reopen the issue.

If you experience other issues with the peptide to PDB mapping, please do not hesitate to open a new issue.