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Messages - eholzhauser

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RNA structures (DSSR) / Re: Redirect Auxiliary File Output
« on: May 13, 2016, 03:20:47 pm »
I apologize for the late reply, but my issue was resolved with the last revised DSSR!


RNA structures (DSSR) / Re: Redirect Auxiliary File Output
« on: May 13, 2016, 11:37:16 am »
I downloaded the Linux 64-bit compiled version on the Downloads page. I still get the same error: "open_file failed: Permission denied".

Thanks for the continued help,

RNA structures (DSSR) / Re: Redirect Auxiliary File Output
« on: May 13, 2016, 10:32:27 am »
I'm using CentOS Linux release 7.2.1511.

Thanks again,

RNA structures (DSSR) / Re: Redirect Auxiliary File Output
« on: May 12, 2016, 04:00:54 pm »
Dr. Lu,

That fit the bill, thank you!

I have a follow-up question, but it may be too ambiguous. Do you know what could cause DSSR to send "open_file failed: Permission denied" to the error stream? I'm assuming DSSR needs read permission to the directory where the input PDB / mmCIF structure is, and read/write permission to the directories where output / auxiliary output are created. When I run the JAR that calls DSSR on my server from the CLI, everything works fine--the auxiliary files and output go where I expect them to. However, when I execute the JAR from the web interface that I'm building, I get that message from DSSR. The web interface runs with permissions set up for Apache, so somewhere, I haven't given Apache the appropriate permissions that I have as a user of the server. So, I am wondering where all I should take care to give DSSR appropriate read/write permissions.

Thanks again, and sorry for the wall of text,

RNA structures (DSSR) / Redirect Auxiliary File Output
« on: May 12, 2016, 02:50:03 pm »
Hello Dr. Lu,

I was wondering if there is a command to redirect the output of the auxiliary files used by DSSR?

I'm developing a web server for RNA 3D structure alignment and am using DSSR for base-pairing annotation. Currently, DSSR always creates the auxiliary files in the directory from which DSSR is called. In my case, DSSR is called by a JAR file in a directory where I don't want to allow write permissions.

Thank you,

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.