Fetch by EMDB via GUI downloads first where before uncompressing in users downloads directory
Hi Chimera,
If I fetch by EMDB via GUI and it downloads then decompresses and freezes where did it go? I know when it is done it goes to my download directory, but where does the gz get downloaded to and where does the partial uncompressed file end up. I cannot find ~5-~10 GB of this lost file. It was ~5 GB gz file so I think the gz is still on my computer. I searched for it to and my computer said no results found so I am not sure if it is named something else when you fetch by EMDB.
Best, Ryan Harlich
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Hi Ryan,
Chimera file fetch uses Python urllib.urlretrieve() which says it creates a tempfile. Where that tempfile would be is operating system dependent and is not in the Python documentation.
https://docs.python.org/2/library/urllib.html https://docs.python.org/2/library/urllib.html
The tempfile is uncompressed and moved to folder ~/Downloads/Chimera/EMDB. Python is responsible for removing up the temporary file and I assume it does that correctly.
Tom
On Jul 31, 2019, at 4:13 PM, Ryan Harlich ryanharlich@hotmail.com wrote:
Hi Chimera,
If I fetch by EMDB via GUI and it downloads then decompresses and freezes where did it go? I know when it is done it goes to my download directory, but where does the gz get downloaded to and where does the partial uncompressed file end up. I cannot find ~5-~10 GB of this lost file. It was ~5 GB gz file so I think the gz is still on my computer. I searched for it to and my computer said no results found so I am not sure if it is named something else when you fetch by EMDB.
Best, Ryan Harlich
Sent from Mail https://go.microsoft.com/fwlink/?LinkId=550986 for Windows 10
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Dear all,
i'm experiencing some problems with the Fetch by ID on the Uniprot database. The error message is Invalid Uniprot accessio number: "about: legacy-compat" The Fetch by ID onto the PDB database works fine. Any suggestions? Thanks Marco
Hi Marco, Did you check that ID at the UniProt website? I tried these fetches that I’d never done before (so the files weren’t already cached locally) and they worked fine.
open uniprot:DMD_HUMAN open uniprot:P08069
So maybe the ID that you entered is obsolete. If you can see that specific entry at the UniProt database but the fetch doesn’t work, then you would have to let us know what ID you used.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 7, 2019, at 6:16 AM, Marco Sette sette@uniroma2.it wrote:
Dear all, i'm experiencing some problems with the Fetch by ID on the Uniprot database. The error message is Invalid Uniprot accessio number: "about: legacy-compat" The Fetch by ID onto the PDB database works fine. Any suggestions? Thanks Marco
In addition to what Elaine says, you need to upgrade your version of Chimera to at least 1.13.1. The UniProt web site changed not that long ago and previous versions of Chimera aren’t compatible with those changes.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 7, 2019, at 7:30 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Marco, Did you check that ID at the UniProt website? I tried these fetches that I’d never done before (so the files weren’t already cached locally) and they worked fine.
open uniprot:DMD_HUMAN open uniprot:P08069
So maybe the ID that you entered is obsolete. If you can see that specific entry at the UniProt database but the fetch doesn’t work, then you would have to let us know what ID you used.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 7, 2019, at 6:16 AM, Marco Sette sette@uniroma2.it wrote:
Dear all, i'm experiencing some problems with the Fetch by ID on the Uniprot database. The error message is Invalid Uniprot accessio number: "about: legacy-compat" The Fetch by ID onto the PDB database works fine. Any suggestions? Thanks Marco
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Hi,
no problems with the new version indeed.
Thanks a lot, Marco
Il 07/11/19 18:46, Eric Pettersen ha scritto:
In addition to what Elaine says, you need to upgrade your version of Chimera to at least 1.13.1. The UniProt web site changed not that long ago and previous versions of Chimera aren’t compatible with those changes.
—Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 7, 2019, at 7:30 AM, Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote:
Hi Marco, Did you check that ID at the UniProt website? I tried these fetches that I’d never done before (so the files weren’t already cached locally) and they worked fine.
open uniprot:DMD_HUMAN open uniprot:P08069
So maybe the ID that you entered is obsolete. If you can see that specific entry at the UniProt database but the fetch doesn’t work, then you would have to let us know what ID you used.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 7, 2019, at 6:16 AM, Marco Sette <sette@uniroma2.it mailto:sette@uniroma2.it> wrote:
Dear all, i'm experiencing some problems with the Fetch by ID on the Uniprot database. The error message is Invalid Uniprot accessio number: "about: legacy-compat" The Fetch by ID onto the PDB database works fine. Any suggestions? Thanks Marco
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participants (5)
-
Elaine Meng -
Eric Pettersen -
Marco Sette -
Ryan Harlich -
Tom Goddard