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Author Topic: Generating .out file  (Read 2494 times)

Offline rooks2181

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Generating .out file
« 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.

Offline xiangjun

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Re: Generating .out file
« Reply #1 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline rooks2181

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Re: Generating .out file
« Reply #2 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?

Offline xiangjun

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Re: Generating .out file
« Reply #3 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 and try to reproduce results there should also prove useful.

Xiang-Jun
« Last Edit: July 22, 2014, 04:40:50 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.