--nogui gets permission denied when fetching pdb id
Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
I wouldn’t be able to say without the actual full error output. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 30, 2019, at 12:01 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui.
Best, Ryan Harlich
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
"permission denied" is usually because you don't have write permission for some directory. Run the "system pwd" command to see which directory chimera is running in. You also need permission for a temporary directory and the download directory. As Eric alluded, the directory that is causing the problem should be obvious from the full error message. HTH, Greg On 7/30/2019 12:31 PM, Eric Pettersen wrote:
I wouldn’t be able to say without the actual full error output.
—Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 30, 2019, at 12:01 PM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent fromMail <https://go.microsoft.com/fwlink/?LinkId=550986>for Windows 10 _______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I get this. Opening 1a1x... [Errno 13] Permission denied: '1a1x' It actually worked in a new folder. But then when I ran my python script it did not work. Then I tried doing it via command line instead of python script and I got the permission denied again. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Greg Couch <gregc@cgl.ucsf.edu> Sent: Tuesday, July 30, 2019 12:42:09 PM To: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu>; Ryan Harlich <ryanharlich@hotmail.com> Subject: Re: [Chimera-users] --nogui gets permission denied when fetching pdb id "permission denied" is usually because you don't have write permission for some directory. Run the "system pwd" command to see which directory chimera is running in. You also need permission for a temporary directory and the download directory. As Eric alluded, the directory that is causing the problem should be obvious from the full error message. HTH, Greg On 7/30/2019 12:31 PM, Eric Pettersen wrote: I wouldn’t be able to say without the actual full error output. —Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 30, 2019, at 12:01 PM, Ryan Harlich <ryanharlich@hotmail.com<mailto:ryanharlich@hotmail.com>> wrote: Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346767145&sdata=qX9OBe3QoGFYYUUMEddkaN3oY1%2FgfL4DEb0hwB4GFzg%3D&reserved=0> for Windows 10 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346777150&sdata=ggD%2BJXTITkRrEXVQzDGWjgCOJghYMXTmgDvi6vRxUZI%3D&reserved=0> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346787161&sdata=fYxrhPbOeV41cPd%2FiKfFu9Mu5lEuIutP%2BGsdqPwLM2s%3D&reserved=0>
It looks like it works before I use os.system(‘mkdir … or os.makedirs or os.mkdir. I am not even in that folder as it is a subfolder I am making. Not sure why it is giving me Errno 13. When I delete the folder it works. But I need to create the folder to save each protein in their folder. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Ryan Harlich Sent: Tuesday, July 30, 2019 12:46:44 PM To: Greg Couch <gregc@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu> Subject: RE: [Chimera-users] --nogui gets permission denied when fetching pdb id I get this. Opening 1a1x... [Errno 13] Permission denied: '1a1x' It actually worked in a new folder. But then when I ran my python script it did not work. Then I tried doing it via command line instead of python script and I got the permission denied again. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Greg Couch <gregc@cgl.ucsf.edu> Sent: Tuesday, July 30, 2019 12:42:09 PM To: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu>; Ryan Harlich <ryanharlich@hotmail.com> Subject: Re: [Chimera-users] --nogui gets permission denied when fetching pdb id "permission denied" is usually because you don't have write permission for some directory. Run the "system pwd" command to see which directory chimera is running in. You also need permission for a temporary directory and the download directory. As Eric alluded, the directory that is causing the problem should be obvious from the full error message. HTH, Greg On 7/30/2019 12:31 PM, Eric Pettersen wrote: I wouldn’t be able to say without the actual full error output. —Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 30, 2019, at 12:01 PM, Ryan Harlich <ryanharlich@hotmail.com<mailto:ryanharlich@hotmail.com>> wrote: Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346767145&sdata=qX9OBe3QoGFYYUUMEddkaN3oY1%2FgfL4DEb0hwB4GFzg%3D&reserved=0> for Windows 10 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346777150&sdata=ggD%2BJXTITkRrEXVQzDGWjgCOJghYMXTmgDvi6vRxUZI%3D&reserved=0> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346787161&sdata=fYxrhPbOeV41cPd%2FiKfFu9Mu5lEuIutP%2BGsdqPwLM2s%3D&reserved=0>
It looks like you can create a folder and then have script create the subdirectories in this folder and be one folder out and it works. Thanks, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Ryan Harlich Sent: Tuesday, July 30, 2019 1:21:56 PM To: Greg Couch <gregc@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu> Subject: RE: [Chimera-users] --nogui gets permission denied when fetching pdb id It looks like it works before I use os.system(‘mkdir … or os.makedirs or os.mkdir. I am not even in that folder as it is a subfolder I am making. Not sure why it is giving me Errno 13. When I delete the folder it works. But I need to create the folder to save each protein in their folder. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Ryan Harlich Sent: Tuesday, July 30, 2019 12:46:44 PM To: Greg Couch <gregc@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu> Subject: RE: [Chimera-users] --nogui gets permission denied when fetching pdb id I get this. Opening 1a1x... [Errno 13] Permission denied: '1a1x' It actually worked in a new folder. But then when I ran my python script it did not work. Then I tried doing it via command line instead of python script and I got the permission denied again. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Greg Couch <gregc@cgl.ucsf.edu> Sent: Tuesday, July 30, 2019 12:42:09 PM To: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu>; Ryan Harlich <ryanharlich@hotmail.com> Subject: Re: [Chimera-users] --nogui gets permission denied when fetching pdb id "permission denied" is usually because you don't have write permission for some directory. Run the "system pwd" command to see which directory chimera is running in. You also need permission for a temporary directory and the download directory. As Eric alluded, the directory that is causing the problem should be obvious from the full error message. HTH, Greg On 7/30/2019 12:31 PM, Eric Pettersen wrote: I wouldn’t be able to say without the actual full error output. —Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 30, 2019, at 12:01 PM, Ryan Harlich <ryanharlich@hotmail.com<mailto:ryanharlich@hotmail.com>> wrote: Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346767145&sdata=qX9OBe3QoGFYYUUMEddkaN3oY1%2FgfL4DEb0hwB4GFzg%3D&reserved=0> for Windows 10 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346777150&sdata=ggD%2BJXTITkRrEXVQzDGWjgCOJghYMXTmgDvi6vRxUZI%3D&reserved=0> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C7c03b69fdc8949cec3c008d715260518%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637001125346787161&sdata=fYxrhPbOeV41cPd%2FiKfFu9Mu5lEuIutP%2BGsdqPwLM2s%3D&reserved=0>
participants (3)
-
Eric Pettersen -
Greg Couch -
Ryan Harlich