3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: ddufour on February 14, 2014, 09:45:04 am

Title: Problem with X3DNA environment variable in Linux installation
Post by: ddufour on February 14, 2014, 09:45:04 am: Hello!

My computer has a 64-bits distribution and runs under Ubuntu 12.04 LTS, and I have ruby 1.9.3p0 installed in it.

When running ./find_pair -h it works fine, but when I tried to run it with an actual PDB fil it happened the following:

david@roy:~/Programs/x3dna-v2.1/bin$ ./find_pair ~/Desktop/1B23.pdb test

handling file </home/david/Desktop/1B23.pdb>
uncommon residue 4SU 8 on chain R [#8] assigned to: u
uncommon residue H2U 20 on chain R [#19] assigned to: u
uncommon residue H2U 21 on chain R [#20] assigned to: u
uncommon residue PSU 32 on chain R [#31] assigned to: P
uncommon residue MIA 37 on chain R [#36] assigned to: a
uncommon residue PSU 39 on chain R [#38] assigned to: P
uncommon residue 5MU 54 on chain R [#52] assigned to: u
uncommon residue PSU 55 on chain R [#53] assigned to: P
uncommon residue GNP 406 on chain P [#486] assigned to: g
open_file <bp_order.dat> failed: Permission denied

So I tried to do it with sudo and this is what happened:

david@roy:~/Programs/x3dna-v2.1/bin$ sudo ./find_pair ~/Desktop/1B23.pdb test
Please set the X3DNA environment variable
Run 'x3dna_setup', and visit http://x3dna.org/ for more info.

I think that I already set up the X3DNA environment variable in my ~/.bashrc, because I added
export X3DNA='/home/david/Programs/x3dna-v2.1/'
export PATH='/home/david/Programs/x3dna-v2.1/bin':$PATH

at the end of the .bashrc file

I don't know what I'm doing wrong, maybe you could help me...

Thanks in advance,
David Dufour
Title: Re: Problem with X3DNA environment variable in Linux installation
Post by: xiangjun on February 14, 2014, 04:35:13 pm: Quote
david@roy:~/Programs/x3dna-v2.1/bin$ ./find_pair ~/Desktop/1B23.pdb test
......
open_file <bp_order.dat> failed: Permission denied
This is weird.

In your ~/Programs/x3dna-v2.1/bin$ directory, run the following:
Code: [Select]
touch bp_order.datWhat do you get back?

Alternatively, just as a test, create a new directory (named x3dna-test) under home, and try the following commands:
Code: [Select]
cd ~ # or simply: cd mkdir x3dna-test cd x3dna-test cp ~/Desktop/1B23.pdb . find_pair 1B23.pdb testPlease report back verbatim what you get in your current settings.

The issue with sudo may be related to the fact that you are switching to another user (root) who does not have the X3DNA environment variable set. Type man sudo for more info.

HTH,

Xiang-Jun
Title: Re: Problem with X3DNA environment variable in Linux installation
Post by: ddufour on February 19, 2014, 05:12:30 am: Hello!

The problem is solved. As you said, I was switching to root, who didn't have the X3DNA environment variable set. I finally installed the program again as my normal user and everything went ok.

Thanks a lot!

David Dufour