Messages

1

RNA structures (DSSR) / Hydrogen bonds between protein and rna in a docked system

« on: March 27, 2017, 10:17:31 pm »

Hi everyone,
I have a quick question about hydrogen bonds-can the program find hydrogen bonds between protein and rna (a docked system)? I have tried using get-hbonds command. However, it only gives me hydrogen bonds in rna-not between protein and rna.
Thanks,
Thanh Le

2

RNA structures (DSSR) / Re: x3dna-dssr installation

« on: March 27, 2017, 10:16:28 pm »

X3DNA-DSSR installation
1) Install x3dna following the steps indicated by Dr. Xiangjun.
2) Download x3dna
3) On Mac OS X or Linux, run the command ‘chmod u+x x3dna-dssr’ to make DSSR executable.
4) Since the path is already set for x3dna, drag x3dna-dssr to the bin folder located in x3dna folder.
5)./x3dna-dssr -h to confirm the installation.

3

RNA structures (DSSR) / Re: x3dna-dssr installation

« on: March 27, 2017, 05:35:31 pm »

Hi Dr. Xiangjun,
I was able to run x3dna-dssr after following your advice. Thank you very much!
I have a quick question about hydrogen bonds-can the program find hydrogen bonds between protein and rna (a docked system)? I have tried using get-hbonds command. However, it only gives me hydrogen bonds in rna-not between protein and rna.
Thanks,
Thanh Le

4

RNA structures (DSSR) / Re: x3dna-dssr installation

« on: March 22, 2017, 09:06:26 pm »

Thank you for the quick response.
Here is the response from terminal:
thanhs-MacBook-Pro-2:bin ThanhLe$ pwd
/Users/ThanhLe/desktop/bin
thanhs-MacBook-Pro-2:bin ThanhLe$ which x3dna-dssr
thanhs-MacBook-Pro-2:bin ThanhLe$ echo $PATH
/Users/ThanhLe/Desktop/x3dna-v2.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Please advice.
Thanks,
Thanh Le

5

RNA structures (DSSR) / x3dna-dssr installation

« on: March 22, 2017, 08:29:45 pm »

Hi Dr. Xiangjun,
I am trying to install x3dna-dssr to my mac; I had successfully installed x3dna. However, I am having trouble to run the program. Using the command line "x3dna-dssr -h" only gives me command not found. Futhermore, double-clicking on the icon, it gives me this
missing required option: must specify -i=PDBFile/mmCIF
type: 'x3dna-dssr -h' for help
What should I do?
Thanks,
Thanh Le
P.S. After downloading x3dna-dssr from the website, I moved it to a bin folder and used the command "chmod u+x x3dna-dssr"