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Messages - MingyuSun

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1
Howtos / Re: How to install 3DNA on Windows?
« on: July 02, 2016, 04:58:31 am »
Dear Mayar12,
I am not sure if you have problem in this step,

echo    'export X3DNA=$HOME/x3dna-v2.3' > .profile
echo     'export PATH=$X3DNA/bin:$PATH' >> .profile
cat     .profile

or you may not install MINGW.

I recorded my experience in For Novice, it might give to some hints.
http://forum.x3dna.org/howtos/for-novices/msg2110/#msg2110
You can just read the following part:
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.

2
Howtos / Re: For Novices
« 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.

3
Howtos / 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/

4
Howtos / Re: How to install 3DNA on Windows?
« on: March 15, 2016, 07:55:03 am »
I tried install 3DNA with Cygwin for several times to finish my homework I left here, only to fail again. I found this topic and I followed, http://forum.x3dna.org/howtos/problem-installing-x3dna-in-windows-with-gygwin/ , in fact, I also tried several changes after the failure, but still succeed. I tried this way too. I put the sreenshots here. What's wrong again?
Quote
Double-click the msys icon to get the shell
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
Close the shell
Double-click the msys icon to open another shell

5
Howtos / Re: usage
« 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?

6
Howtos / Re: usage
« 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!

7
Howtos / Re: How to install 3DNA on Windows?
« on: March 12, 2016, 12:41:17 am »
I am sorry for failing to notice your reply in time again. As for the summary, I will definately do with pleasure! 3DNA is a great work! Could I leave that for my birthday on Mar. 20th, since I have been doing something myself in celebration for the day ever since I was 17? And this year, I want to do the summary for my birthday. Before that, I will enjoy my journey, trying to get more about it and providing more information at that time.
But I can also do it right away if you hope so.

Yours
Mingyu

8
Howtos / Re: How to install 3DNA on Windows?
« on: March 11, 2016, 10:13:56 pm »
I am really grateful for you! I am very excited now! Thank you very much for your great creation and patience! I am exploring happily now!

9
Howtos / Re: How to install 3DNA on Windows?
« on: March 11, 2016, 09:14:47 pm »
Sorry for that and sorry for failing to notice your reply in time, which may due to that I forgot to choose the e-mail notification. There may be something wrong for me. If I double-click the msys icon to get the shell and type the commands, I will see fig. install 04. And then I close the shell,
double-click the msys icon to open another shell, type "fiber -h", I will see install 06. I also tried to do the first three steps of installation, and type the commands you gave me in the reply, that is fig. install 05, but I meet the same case as fig. install 06.

10
Howtos / Re: How to install 3DNA on Windows?
« on: March 11, 2016, 09:05:31 am »
I am sorry for keep bothering you for silly question. After I run"./x3dna_setup", I can't do the key parts colored red. I put my case in the attachments. I can't find ~/.profile. is it just be in linux? It seems that I can't find that under windows.

11
Howtos / 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。

12
Howtos / Re: Install 3DNA on Windows via MinGW/MSYS
« on: March 08, 2016, 07:11:27 am »
I am really grateful for your kindness and patience! Thanks a lot! I think I have installed it. I am still trying to learn about the usage. Anyhow, I already have a great time time with it. You can't image how happy I am. And I will do the homework you left for me.

13
Howtos / Re: Cannot install 3DNA on Windows
« on: March 07, 2016, 12:54:30 am »
I finally install cygwin using default, but I can't run it. I show my case in attachment.

14
Howtos / Re: Install 3DNA on Windows via MinGW/MSYS
« on: March 07, 2016, 12:36:14 am »
I am really sorry, I have not got that done. I tried three times, including try to reopen the shell after extracting the x3dna. A difference is the /home/ in my case. I showed you in the attachment.

15
Howtos / Re: Install 3DNA on Windows via MinGW/MSYS
« on: March 06, 2016, 09:24:14 pm »
I am really sorry that I just noticed there is another question.
I just try, and I attached the outcome here. I also tried tar --help and tar --usage, many others will appear after that.

16
Howtos / Re: Install 3DNA on Windows via MinGW/MSYS
« on: March 06, 2016, 09:03:20 pm »
It is really kind of you!
1,I have two laptop, one is window7, another is window10, I mainly used window7, but I can try both if needed.
2,I put the download file both in C and D, as showed in the attachment.(if I need to used it in another laptop with window 10, there seems to be only one disk.
3,I have not. Sorry. I know nothing about tarball file, I am searching for it now.

17
Howtos / Re: Cannot install 3DNA on Windows
« on: March 06, 2016, 08:23:13 pm »
Thanks very much!
I might have install MinGW, I got an icon of it. I put my case in the attachment.
I failed to install Cgywin yesterday, it is the same case as the attachment above. I am still trying to install it now. But can I just use the default, rather than pick up packages myself? I also put the screenshot here.

18
Howtos / Re: Cannot install 3DNA on Windows
« on: March 06, 2016, 07:54:54 pm »
May be yes. I presumed it was because that the fiber is in 3DNA v2.3, I can't use that command with only DSSR, is that right?
So how should I install 3DNA v2.3 now?

19
Howtos / Re: Cannot install 3DNA on Windows
« on: March 06, 2016, 07:39:47 pm »
Dear Dr. Lu,
Thank very much!
To be honest, I haven't intalled that successfully yet, I can only running it with cmd. I may have not found out the right place for running the command. I put it both in D\DNA, and C\bin. I showed my situation in the screenshots. If I didn't not open cmd and verify the path, it seem that things would not work. And I can run fiber -rna -seq=AAAAUUUGGGGCCCC fRNA.pdb successfully.
I am really grateful for your replys, I tried to find others for help, they are very kind, but failed to help me out at last.

20
Howtos / Re: Cannot install 3DNA on Windows
« on: March 06, 2016, 07:58:44 am »
Dear Dr. Lu,
Sorry for my failure again. To be honest, I kept trying to install Cygwin, but instead of chosing the default,  I follow the tips here,http://www.33lc.com/article/7276_2.html. I can't find gcc-mingw, so I chosed other packages including mingw. However, I kept failing. I put my case in the attachment, it is the same thing everytime. And this has been repeated for several times. Is that because of my network? I rely on the campus-network which is slow these days.
I really hope I can make it and send a screenshot of successful installation to you. Sorry!
I am really grateful for your advice and I will definitely review this experience. Anyway, I enjoy it.

Yours
Mingyu

21
Howtos / Re: Cannot install 3DNA on Windows
« on: March 06, 2016, 03:57:22 am »
Maybe I have install MinGW successfully, but I still can't install 3DNA. I put my case in the attachment. There is icon named MinGW shell.

22
Howtos / Re: Cannot install 3DNA on Windows
« on: March 06, 2016, 01:33:26 am »
May be I should also put this screenshot here. Besides, is there manual for 3DNA v2.3?

23
Howtos / Re: Cannot install 3DNA on Windows
« on: March 06, 2016, 01:12:07 am »
Thanks very much!
When I install cygwin, which packages should I intall? I put the sreenshot in the attachment.

24
General discussions (Q&As) / Re: PDB file for Gaussian
« on: March 05, 2016, 06:17:06 am »
I am really sorry keep bothering you. But in fact, I have not successfully install that. I tried to run it with cmd, but failed. I tried to install MinGW Ruby, I should have installed them.When I click MinGW, I got a screen, but I still cannot install 3DNA v2.3. I put two screenshots in the attachments explaining my situation. I do not know why I can't paste them here directily.
As for the MinGW, there are two potential problems. I did not see "blur" as mentioned on the website. And there is only one "fstab.sample" that cannot be opened in the place that "fstab" should be, I created a txt name "fstab" and only wrote C:\MinGW   /mingw there.
Do you know how to fix that?

25
General discussions (Q&As) / Re: PDB file for Gaussian
« on: March 05, 2016, 12:59:23 am »
Thanks a lot! I will.
I just tried some PDB file in x3dnav2.3\examples\analyze_rebuild, some can work with Gaussian, (some other PDB file in x3dnav2.3 can as well). I don't know why. But could I use this materials, I mean x3dnav2.3, to make change for my original one directily?

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.