3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: rooks2181 on July 16, 2014, 01:07:15 pm

Title: Generating .out file
Post by: rooks2181 on July 16, 2014, 01:07:15 pm: Hi, I think I've gotten 3DNA running properly locally using Cygwin. In the past I've used web 3DNA and then worked with the provided .out file. What is the command using 3DNA locally to produce the same .out file provided by the web version? I believe it's 'find_pair', but with what options? Let's suppose we're working with file 1EHZ. I've attached the .out file that I want to be able to produce locally. Thanks in advance for your time and help.
Title: Re: Generating .out file
Post by: xiangjun on July 16, 2014, 06:05:24 pm: The .out file is generated by running the find_pair/analyze pair of 3DNA programs, as below:

Code: [Select]
find_pair 1ehz.pdb 1ehz.bps analyze 1ehz.bps
You will have file 1ehz.out, along with a few other files.

HTH,

Xiang-Jun
Title: Re: Generating .out file
Post by: rooks2181 on July 22, 2014, 04:17:12 pm: Thank you, Xiang-Jun. I'm curious - are there instructions somewhere that would have helped me know that?
Title: Re: Generating .out file
Post by: xiangjun on July 22, 2014, 04:24:37 pm: Does the $X3DNA/doc/x3dna_v1.5.pdf manual help? Read carefully the 3DNA 2008 Nature Protocols paper (http://www.nature.com/nprot/journal/v3/n7/abs/nprot.2008.104.html) and try to reproduce results there should also prove useful.

Xiang-Jun