Messages

1

General discussions (Q&As) / Re: Problem with X3DNA environment variable in Linux installation

« 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

2

General discussions (Q&As) / Problem with X3DNA environment variable in Linux installation

« 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