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Author Topic: usage  (Read 1899 times)

Offline MingyuSun

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usage
« on: March 11, 2016, 07:25:27 am »
I still have not found out why I can't use some commands. It seems that there are on my command search path, and in the shell.  Is that because I haven't set x3dna environment variable? If it is, then how to set it? I put my situation below。
« Last Edit: March 11, 2016, 07:40:57 am by MingyuSun »

Offline xiangjun

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Re: usage
« Reply #1 on: March 11, 2016, 08:13:15 am »
You've not set up 3DNA successfully yet, at least with respect to setting the X3DNA environment variable. See instructions at How to install 3DNA on Linux and Windows?. Specifically, you need to:

Code: [Select]
cd x3dna-v2.3/bin
./x3dna_setup

Follow the instructions of x3dna_setup output.
« Last Edit: March 11, 2016, 08:19:11 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline MingyuSun

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Re: usage
« Reply #2 on: March 12, 2016, 07:10:18 am »
Dear Dr. Lu,
I had a great time with your creation!
There are some questions.
1, as for "rebuild" is that just transforms one file from a kind of format to another? I mean, could it also transform a B-form to A-form or another form?
2, if I want to get a doped DNA, could 3DNA generate one? I have not found related command.
3, I had problem using blocview, mstack2img, cp_std, I put a sreenshots here. As for the cp_std, is that because it can only be used as "x3dna_utils cp_std"
4, I do not know why, the PDB file can't be open by Gaussian03, or I should say, it can't be converted into gif. file by using Gaussian03. However, I opened that with GaussView05, and even saved the file, though I have not submitted yet, because of my campus network.  I will see, anyway. (there is another case for Gaussian, but I failed to reproduce it just now)
Again, thank you very much!

Offline xiangjun

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Re: usage
« Reply #3 on: March 12, 2016, 10:20:24 am »
Please ask your question ONE at a time on the General Discussions (Q&As) section, starting from the simpler one most relevant to what you want to achieve. As noted in the README file distributed with 3DNA v2.3, you're welcome to reproduce the protocols reported in the 2008 3DNA Nature Protocols paper to get a sense as to what 3DNA is about.

Enjoy your journey. Learn from and contribute back to the Forum (an virtual community).
« Last Edit: March 12, 2016, 10:29:02 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline MingyuSun

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Re: usage
« Reply #4 on: March 13, 2016, 09:43:17 am »
Thank you very much! I just read that and gained more insight to 3DNA, I will try to reproduce it soon.
As for those questions I posted, if you do not mind, I hope to take my time, though I can post it one by one from now on. Personally, I just feel like trying by myself when I really use it first.
I have been trying to open this website http://3dna.rutgers.edu/,but failed. It is likely that my network should be blamed, but is there any other problems?
By the way, would you mind me putting the full text of the paper in 2008 in the attachment when I write the summary?

 

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.