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Author Topic: For Novices  (Read 1622 times)

Offline MingyuSun

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For Novices
« on: March 20, 2016, 03:47:03 am »
Overview:
3DNA is for analysis, rebuilding, and visualization of three-dimensional nucleic-acid-containing structures, including their complexes with proteins and other ligands, featured in purely geometrically based and that it allows for exact construction of a model from a set of straightforward and well understood, user-supplied parameters (ref01). x3dna-dssr and x3dna-snap are separated downloads but can work together with 3DNA

Installation:
Register at the 3DNA Forum, Log in, click Downloads and 3DNA download. Download 3DNA (like 3DNA version v2.3-2016jan20, (ref02)) x3dna-dssr and x3dna-snap if you need. (If you are not sure, download all of the three, they are not big.)
Since most novices work under windows as me, here, I just focus on window version.
Regarding your choice between MinGW/MSYS, and Cygwin, you can refer the website, or the following quote: Cygwin seems more Linux-like, whilst MinGW is more Windows-like (ref 03).

After you download 3DNA (or other two mentioned above), do not depress them directly and try to double click ~.exe, which is useless, though you can find them. You might notice that the file you download is a little strange, namely, it is x3dna-v2.3-mingw-win.tar.gz. It seems that those with ~.tar.gz shall be run in a Unix/Linux environment, different from those we are familiar with under windows. This point is addressed in ref01. Anyhow, you can’t install or use this way, you have to get MinGW or Cygwin at hand first. And this file must be put in the shell.

Installation with MinGW
1, install msys
•   Following the link Getting Started, download the GUI installer 'mingw-get-inst'. Use defaults options, except at the "Select Components" section, be sure to pick "MSYS Basic System" so that both MinGW and MSYS are both installed at the same time.
•   Then install the latest version with Ruby (v1.9.3) with "Ruby Installer". In the "Installation Destination and Optional Tasks" section, be sure to select "Add Ruby executables to your path", and "Associate .rb and .rbw files with this Ruby installation".(ref04)
Notice:
1, there is a detailed instruction here, the only difference is that I did not see “blur”, but I presumed that it was not a serious problem since I installed successfully at last.
http://www.mingw.org/
2, if you can only see MinGW installer icon (fig.MinGW01), you have not installed it, you should see MinGW shell icon (fig.MinGW02) after successful installation.
3, double click MinGW installer icon (fig.MinGW01), make sure you pick "MSYS Basic System", then, chose “Apply Changes” in the Installation in the upper left, you can get MinGW shell icon (fig.MinGW02)

2, install Ruby
http://rubyinstaller.org/downloads/
You can find it there, and since there is one installer for the case that you are not sure yourself, novices should be able to cope with that. Just follow the quoted instruction.

3, install 3DNA
1, double click msys icon to open a new shell, type ‘pwd’, which show your home directory (mine is /home/Administrator)
 '/home/administrator' is your home directory. On Windows, it should be in C:\MinGW\msys\1.0\home or something like that. (ref05) not C:\Users\Administrator.
2, move (or copy) the downloaded file (tarball x3dan-v2.3-mingw-win.tar.gz) into your home directory (depression is not needed), that is C;\MinGW\msys\1.0\home. If you did it correctly, you would see something after typing “ls –l”(lower case L) in the shell.
3, run “tar zxvfp x3dna-v2.3-mingw-win.tar.gz”
4, run “cd x3dna_v2.3/bin (or other ~_v~)
5, run “./3dna_setup”
6, as for the instruction get see (fig.install01,the upper part),
1.   Double-click the msys icon to get the shell
2.   Within the opened terminal, type the following commands strictly:
Quote
echo    'export X3DNA=$HOME/x3dna-v2.3' > .profile
echo     'export PATH=$X3DNA/bin:$PATH' >> .profile
cat     .profile
3.   Close the shell
4.   Double-click the msys icon to open another shell
5.   In the opened terminal, type: fiber –h (or other command with –h)
Notices:
1, Pay attention to the space in the quoted command
2, you can try tar, tar --help, car --help in the opened shell, which will give you much more information (personally, I have not made them clear to me)
3, copy (or move) x3dna-dssr.exe, x3dna-snap.exe into C:\MinGW\msys\1.0\home\Administrator\x3dna-v2.3\bin though they can also be run with cmd(fig.dssr01)
By the way, you can get cmd by using windows+R or in the “start”, searching for it is OK.


As for Cgywin

1, install Gqywin
https://cygwin.com/
manual and many other information can also be found here. The manual is here: https://cygwin.com/cygwin-ug-net/cygwin-ug-net.pdf
And some tips like this one can be found online.
http://cs.calvin.edu/curriculum/cs/112/resources/installingEclipse/cygwin/
But you may not be able to select some packages in the Devel. I guess that is because you have not had some components installed. (You can also consult the manual. As for the mirror, refer to https://cygwin.com/mirrors.html)
It is very kind of Cesarzapata to post the experience on the forum, which is very clear. 
http://forum.x3dna.org/howtos/problem-installing-x3dna-in-windows-with-gygwin/
Unfortunately, I did not succeed following this, and have not found out why yet. I guess I need to read the manual first, which I have not finished, and I have not found “Cygwin-specific documentation in the /usr/share/doc/Cygwin/ directory” mentioned in the manual.
All in all, I am pretty sorry for failing to provide more detailed information here, but I think I will in the future, and I hope other can also join me.

I do not know why so many things work under linux at first. But now, as far as I see, the following two may be the points:
1, it is more stable;
2, it is more portable ( can work with anything with Unix);
so it is up to you if you are to face up with the forbidding linux, if you are bound to focus on simulations, may be you have to.


Usage
After successful installation, you can type command you already knew with –h to get a detailed information about the command, and related commands will appear in “see also”. You can type them with –h if you want. Beside, you can go C:\MinGW\msys\1.0\home\Administrator\x3dna-v2.3\bin, and decide ~ -h with the hints you see (those with.exe)
I suggested you having a try instead of just reading those information, so that you can understand them. i.e. fiber -rna -seq=AAAAUUUGGGGCCCC fRNA.pdb this command means creating a PDB file for AAAAUUUGGGGCCCC RNA named fRNA.
 
Another way to explore it is by reproducing the protocols in 3DNA: a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures which I put in the attachments.( http://www.nature.com/nprot/journal/v3/n7/abs/nprot.2008.104.html) But you will need some third-party tools including MolScript, render in Raster3D, convert of  ImageMagick and so on, which is addressed in the paper. I have not got all of them myself, but I think I will in the future (I have not successfully reproduce 3 and 4, in fact, I can’t run blocview -t=300 -i=2acj_dna.png 2acj_dna.pdb and some other commands because of the lack of related software). I may also put my experience here. Again, join me! Even not having got everything ready, some can also be reproduced. I suggest you having a try since it gives novices a clearer view of both the paper itself and 3DNA.
Some tips for reproducing the protocols in the paper:
1, go to C:\MinGW\msys\1.0\home\Administrator\x3dna-v2.3\np_recipes\R1_diagram, or C:\MinGW\msys\1.0\home\Administrator\x3dna-v2.3\np_recipes\R~_diagram, to get some materials you need in the recipes, namely, copy or move them into C:\MinGW\msys\1.0\home\Administrator and then you can proceed following the direction of the recipes. But instead of copying all of them at one time, I advice you just get one file ready at a time.
2, in 1egk, the first is one rather than lower case of L, I remember there are other cases that are a little confusing, but you can just have a try like this example.
3, managing your screen may increase your efficiency. If you have two screens, you can try windows+p, if you only got one, you can try windows+left/right to divide your screen.
4, during or after your reproducing experience, you can refer to PROCEDURE in the paper to get a better understanding.

The output can be find here: C:\MinGW\msys\1.0\home\Administrator, your home directory.
Before typing the commands you find in the paper or other resource, you’d better type that keyword+-h first. For example, for” rebuild -block2 propeller.dat propeller.alc” you may get a general view of “rebuild” by using “rebuild –h”.
If you are going to do simulations with the PDB files generated by 3DNA, by fiber, to be specifically, it seems that you need to add H. Personally, I constantly failed to open the PDB files produced by 3DNA with Gaussian, but I can open it with GaussView, anyhow, Gauss should be able to add H. if you just have Gaussian, but not GaussView, you can open it with Notepad++, the information there may help you get gif file (but I have tried to make such file myself, you will know why after you open this way). I am also a novice regarding Gaussian, and haven’t launched such simulations due to lack of access to server cluster, but I will in April, and I may post useful experience or more likely, questions on the forum then.
Apart from GaussView and the sofewares method in the paper, you can also open the PDB file with VMD and Material Studio (MS may not be suitable). But my own experience is too limited to provide you more regarding software nor differences between these software.

There is a web-interface which may meet the general needs
http://w3dna.rutgers.edu/
If you just want a PDB file, go the following page directly
http://w3dna.rutgers.edu/rebuild/

I should have put them at the beginning, but I deliberately placed them there, simply to invite you to have a try. I am totally a novice in this aspect and many related aspects. No one around me do similar research, no one has ever used Gaussian, msys, Cgywin, let alone 3DNA, rendering me to a situation with little assist apart from the forum and limited resources I can find online, I even do have access to google. Besides, I have to go to the hospital constantly, prepare for my defense thesis for my BA (on 31th, Mar.), an important exam (luckily, on 19th, Mar.), deal with chores. Considering these, I am convinced that most can get at least this stage, and probably much further and better than me. Though you may meet problems, don’t give up, and you will definitely find it worthwhile. In my case, I underwent an unsuccessful surgery on 17th’, then an exam, when I came back to my work and began this summary on 19th, I was relieved, though I still fumbled at it. I guess exploring itself, as long as it is related to your interest, is home to us.
I write this summary for novices with similar interests, for Dr. Lu. Thanks for his creation, patience and generous help. May be Dr. Lu created 3DNA with his soul, since he devotes so much to it.
Last but not least,
Quote
Learn from and contribute back to the Forum (an virtual community).
Limitation:
I feel quite sorry for failing to explore enough for you since I was constantly distracted by other things. Fortunately, I think I will be able to concentrate on my interest in the near future, I will try to post more in the future. But as I want to keep my promise both to Dr. Lu and to myself, I finally put this limited one here today.
Most of this summary is not original, you can find the information in the ref. though I may fail to point every points clearly in the context of the summary. Some may have not been listed clearly, but all can be found in Howto on the forum. I intended to fix it, however, the network has been a headache for me. I nearly failed to post this one today.
Most information provided by Dr. Lu, they should be correct, but there is some by myself, these are not necessarily correct. I can only say I believe they are, and once I found anything wrong, I would notify it. Any suggestions and notification for this work is welcomed.
I put two PDF files in the attachment, if this action is not appropriate (I have not asked for permission), please contact me.
Sorry for being verbose, and if I failed to make it clear to you, please let me know. Again, any suggestion or notification is welcome.
Reference
1 Xiang-Jun Lu and Wilma K. Olson. 3DNA: a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures. Nature Protocols 3, -1213 - 1227 (2008)
http://www.nature.com/nprot/journal/v3/n7/abs/nprot.2008.104.html
This can also be found in x3dna-v2.3-mingw-win.tar.gz, the downloaded file, (~\x3dna-v2.3-mingw-win\x3dnav2.3\doc, together with others)or on researchgate, if you lack access to that.
2, http://forum.x3dna.org/site-announcements/download-instructions/
3, http://forum.x3dna.org/howtos/problems-with-installing-3dna-on-mingwmsys/
4, http://forum.x3dna.org/howtos/how-to-install-3dna-on-linux-and-windows/
5, http://forum.x3dna.org/howtos/install-3dna-on-windows-via-mingwmsys/
« Last Edit: July 02, 2016, 04:49:31 am by MingyuSun »

Offline xiangjun

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Re: For Novices
« Reply #1 on: March 20, 2016, 12:54:27 pm »
Thanks for the long summary post. Your difficult experience in installating 3DNA is certainly the extreme in my supporting of the software for 15+ years. I am impressed by your strong desire and keen interest to learn.

At this stage, your may want to focus on using 3DNA via MinGW/MSYS. If you insist on installing 3DNA on Cygwin, please start a new thread with your questions. The general instruction in How to install 3DNA on Linux and Windows? should help get you started. Just pay attention to details (especially any error messages).

Xiang-Jun
« Last Edit: March 20, 2016, 01:17:12 pm 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: For Novices
« Reply #2 on: March 21, 2016, 01:22:46 am »
Again, thanks for your patience, your generous help and the joy and relief 3DNA gave me.
The difficult experience should blame on myself. To be honest, I even have difficulty on Cgywin. I am considering if I should try to work with Cgywin or Linux, or how much I should learn about them. In fact, I never have real experience regarding DNA, neither have people around me now. My interest began from Pro. Nongjian Tao and Pro. Bingqian Xu's work, which is mainly about experiments. I still believe I will focus on experiments now, as I stated during my interview. After I finally became a PHD student of Pro. Xu, I got the simulations as my first task. Before I can reach my supervisor in Aug. , this is likely to be the only homework he gave me. Personally, though I still hope to focus on experiments, I am also considering undertaking simulations at the same time, just for the joy and larger freedom it can give me.
This is my case, so could you give me some advices regarding Cgywin, Linux, or simulations. But if it is bothering, you are not necessary to reply since I presume this will not be an usual case.

 

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.