Messages

1

Site announcements / News items -- What's happening in the forum?

« on: October 04, 2011, 05:14:29 pm »

As the number of topics in the forum increases, I think it helps to have a summary post so occasional viewers can know what's going on. This "News Items" post outlines topics that (I feel) are worth mentioning.


• The v2.1beta is updated to fix a bug for structures containing non-DNA/RNA backbone [2012-02-28].
• It is now much easier to download 3DNA -- simply register in the 3DNA forum, and login to see the post containing the download links [2012-02-25].
• A new thread started by Dr. Wilma Olson on 3DNA's analysis of the four distinct forms of duplexes should be of general interest [2012-02-24].
• A new section titled "Bug reports and feature requests" has been created [2011-12-04].
  
• The thread "Ruby scripts for the analysis of MD simulation trajectories" is split. The initial announcement has been followed with many Q&A posts, creating too long a thread that spans over "two pages" [2011-10-16].
  

Xiang-Jun

2

Site announcements / Further notes on forum registration and posting

« on: November 05, 2010, 11:56:35 pm »

This post is out of date, and is kept here for the record.

Over the past few months, upon request I have activated many new registrations for the 3DNA forum. To my surprise, however, very few of those newcomers have posted, certainly at a much lower percentage than perviously. As I've (hopefully) made clear in the several posts in the "Site announcements" section (see below), the content of the forum is open to public for viewing. Thus, unless you would like (and strongly encouraged) to get more actively involved, i.e., to post in the forum, there is really no need to register.

Note that the 3DNA forum is not a mailing list. According to the wikipedia entry on "Internet forum":

One significant difference between forums and electronic mailing lists is that mailing lists automatically deliver new messages to the subscriber, while forums require the member to visit the website and check for new posts. ... Visiting and participating in forums normally requires no additional software beyond the web browser.

Technically (and specifically), the 3DNA forum does not have email functionality. Thus, even those with active registrations cannot receive emails, or communicate with each other (including to the admin) by sending messages, directly through the forum.

As stated in my "Welcome message", this forum was created to make 3DNA-related "Q&As open to the community, archived and searchable". By making the content public, I've been putting pressure on myself to respond professionally. On the other hand, you may (as is often the case) choose to remain anonymous by not revealing identifiable information with your registration.

To make the forum spam free, some rules must be enforced, but they all boils down to just follow common-sense "netiquette". Over the years, I have strived to "make the 3DNA forum a more pleasant virtual community for all of us to learn from and contribute to".

Welcome  to register, but more importantly, do not hesitate to post! After all, that's the whole point to register.
 
Xiang-Jun Lu, the 3DNA forum administrator

3

Site announcements / NAR featured article by Lu et al.: the GpU story

« on: March 12, 2010, 01:13:36 pm »

We have just got a new 3DNA-related paper by Lu et al. published in NAR:  "The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex". Better yet, this paper has been selected as a featured article! According to the NAR website:

Featured Articles highlight the best papers published in NAR. These articles are chosen by the Executive Editors on the recommendation of Editorial Board Members and Referees. They represent the top 5% of papers in terms of originality, significance and scientific excellence.

In addition to its scientific significance (observation of a novel out-of-plane backbone 'edge'; first example on the RNA sugar-phosphate backbone specificity), this paper should serve as another example of what 3DNA could do (in the right hand), and help to answer the question "Does 3DNA work for RNA?"

For a little more background information about how the GpU story got started, you may be interested in reading my blog post, "What's special about the GpU dinucleotide platform?"

Xiang-Jun Lu

4

Site announcements / On maintaining the 3DNA forum

« on: October 30, 2009, 09:42:16 pm »

This post is out of date, but contains valuable background information and thus kept here for the record.

Note: Recently, I have heard from a few users that they cannot follow the "README!" link (upper right corner in the 3DNA forum) to my blog post titled "On maintaining the 3DNA forum" because blogspot (of Google) is blocked in China (maybe in other countries/areas as well). The blog post, however, contains important message that I want to get across to the community, especially to new 3DNA users. Nevertheless, I do not want to repeat the basic rules repeatedly. Thus, I have duplicated the blog post here and re-directed the "README!" link to the 3DNA forum.

Over the past few years, maintaining the 3DNA forum (i.e., answering questions, performing administrative tasks) has taken up a significant amount of my spare time. Sometimes it could be quite demanding, especially because I need to pay great attention to details. Overall, though, it is a valuable experience, and I feel that the time is well-spent: 3DNA has been continuously refined and more widely used; my knowledge of nucleic acid structures (especially RNA) has been significantly sharpened; I have stayed aware of progress in related research fields and see more of the world; and I feel great pleasure in being of help to the community.

Some basic facts/statistics:

• I tell everyone who sends me email to ask 3DNA-related questions to register and re-post in the 3DNA forum, but less than 50% actually do this. However, if you want to be helped, you have to follow the rules.
• Most of the forum registrations (over 90% at times) are spam. To forestall this, I must continually update phpBB3 to its latest version.
• Over 50% of legitimate registrations end up being deleted instead of being activated due to the users' failure to send me an email for activation, as required. Among those whose send me an email, most use a subject line of "Re: 3DNA forum registration — 'user-id'", as suggested. Only a few volunteer to share with me their real name, address, etc. (e.g., via a signature). Furthermore, some do not post back in the forum after their account is activated.
• With very few exceptions, questions posted in the forum are normally addressed within a couple of days, or even sooner.
• Except for one case, communicating with users has mostly been a pleasant experience. Some (though not many) users even posted back a summary and/or a thank-you note.
• I would like to compliment esguerra, yrxin and tgaillar for sharing their tips and tricks in the section Users' contributions. Apart from me, ghzheng has contributed the most in the forum.
• Overall, the forum is low volume (which is just fine) and spam-free (which is very important).

To make the forum policy upfront and explicit in order to avoid misunderstandings or surprises, I have been enclosing the following note in each new registration confirmation message:

Your 3DNA forum registration has been activated — welcome aboard! See
http://xiang-jun.blogspot.com/2009/07/on-maintaining-3dna-forum.html

---------------------------------------------------------------------
I am so pleased that you have come thus far! To make the 3DNA forum a
more pleasant virtual community for all of us to learn from and
contribute to, please be considerate and practice good netiquette
(http://www.albion.com/netiquette/). More specifically, I would like
to reemphasize the following:

0. Do your homework; read the FAQ and browse the forum.
1. Ask your questions in the 3DNA forum instead of sending me emails.
2. Be specific with your questions; provide a minimal, reproducible
   example if possible; use attachments where appropriate.
3. Do not ask for or expect immediate responses to your questions.
   Lower your expectations and you will more likely end up feeling
   happier.
4. Respond to requests for clarifications.
5. Summarize the solution to your problem(s) from a user's
   perspective by providing details, for the benefit of other users.
6+ Contribute back to 3DNA if you can:
   o Report bugs — including typos
   o Make constructive suggestions — anything to make 3DNA better
   o Answer other users' questions
   o Share your use cases in the "Users' contributions" section

In a nutshell, you are welcome to participate and should not hesitate
to ask questions, but remember to play nice and preferably share what
you've learned!
---------------------------------------------------------------------

Thus, intentionally or otherwise, the forum has also acted as a filter to make my life easier. Whenever possible, though, I have tried my best to reward those who follow the simple, common sense rules. After all, nothing should be taken for granted, and no one likes to be taken advantage of. I am glad that through my contributions and user involvement, the forum has survived and 3DNA has thrived (evident from citations, numerous web links to its homepage, other services/tools — including NDB and PDB — taking advantage of its functionality, and more recently, two dedicated web-interfaces), serving as a valuable resource to the community.

5

Site announcements / With w3DNA, using 3DNA can't get easier!

« on: April 06, 2009, 05:01:02 pm »

Hi,

We are pleased to announce that w3DNA -- the web server interface to 3DNA is now available. No registration, no login, no download, w3DNA is designed with GUI inclined users in mind, and could serve as a handy tool for education purpose as well. With w3DNA, the most commonly used 3DNA v2.0 functionality (for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures) is now approachable to anyone on the internet!

Enjoy using w3DNA! If you have any questions, please post them at section w3DNA web server topics. w3DNA has been developed by Mr. Guohui Zheng, a graduate student in Dr. Olson's lab at Rutgers.

Xiang-Jun

6

Site announcements / How to download 3DNA v2.0?

« on: March 16, 2009, 08:25:31 pm »

This post is by far the most viewed. It has served its role and is now out of date. It contains information still of interest, and is kept here for record. Now download 3DNA is much easier for every one!

The latest 3DNA v2.0, with scripts and associated data files accompanying our Nature Protocols (NP) publication [vol.3, no.7 (2008), 1213-1227] (with the NP_Recipes directory content available without restrictions), is distributed in tarball files for the most commonly used operating systems that I have access to (see list below). Please check this thread for more background information and to understand why you should upgrade to 3DNA v2.0. You may also find it worthwhile to read my blog post on 3DNA vs. Curves+, a successor of the well-known Curves program.

Due to the licensing policy imposed by Rutgers, however, I cannot distribute 3DNA v2.0 as simply as for v1.5. So I have put the v2.0 tarballs in a password-protected directory and furnished Rutgers with access details. Please contact Dr. Wilma Olson (wilma.olson AT rutgers DOT edu) for instructions on license, registration and download of 3DNA v2.0. You may want to mention the 2008 3DNA NP paper regarding the availability of v2.0 for others to verify reported results. Please also CC your email request to 3dna.lu AT gmail DOT com (just for my record), and post any issues you experience in this forum.

• Linux (32 bit; Ubuntu 8.04) (should also work on other Intel-based Linux systems)
• Intel-based Mac OS X (thanks to Ben Eisenbraun, Structural Biology Grid, Harvard Medical School)
• Mac OS X (PowerPC)
• Cygwin on Windows (see Cygwin homepage for details)
• Native Windows binaries with MinGW (see MinGW homepage for details; you may also want to have MSYS installed)
• SunOS 5.9
• SGI IRIX64, compiled with gcc
• SGI IRIX64, compiled with native cc (-n32 option, thanks to Tom Chapin at Rutgers University)

As always, I appreciate your comments, suggestions and bug reports on 3DNA (v2.0). Specifically, I would strive to get back to you (through the 3DNA forum), quickly and concretely, on every question regarding any technical details that led to the results reported in our 3DNA 2008 NP paper. In my opinion, the most effective way to learn what 3DNA has to offer is by repeating all the "recipes" and understanding how each one works thoroughly.

In the current context, it is well worth noting that being responsive is one of the core principles that I have always followed in support of 3DNA and maintaining the forum in my (limited) spare time, no matter what users' questions have been. It is my understanding from the very beginning that getting 3DNA (or any serious software product, for that matter) published is just the beginning. In the long run, it is the continuous refinements of the software, as driven by its user community, that make a real difference.

Thanks for your interest in 3DNA – I hope you enjoy using it!

Xiang-Jun Lu

PS: Composite image of the eight figures in the 2008 3DNA Nature Protocols paper:

7

SCHNAaP/SCHNArP / Re: SCHNArP/SCHNAaP c source code

« on: March 15, 2009, 01:13:46 am »

I have just went through the code (it was a piece of work 10+ year ago!), and made some minor changes to make the code compile happily with today's gcc. A separate email I am sending to you contains download instructions. Please share with the community by posting back here any issues you have with the code.

Xiang-Jun

8

SCHNAaP/SCHNArP / What and why re: SCHNAaP/SCHNArP

« on: March 15, 2009, 01:07:40 am »

This is the 3DNA forum, so why SCHNAaP/SCHNArP? What are they anyway?

SCHNAaP/SCHNArP is a software package for the analysis and rebuilding of double helical nucleic acid structures. It was developed during my PhD research with Dr. Chris Hunter at the University of Sheffield back in middle 1990s. Among other functionalities, it implements the simple and elegant Calladine and El Hassan Scheme (CEHS) for calculating a set of local helical step parameters, and reversibly, for rebuilding a structure from such a set of parameters. The theme of my thesis is on sequence-dependent DNA base-stacking interactions, and the CEHS scheme allows me to make a rigorous comparison of my theoretical calculations with oligonucleotide X-ray crystal structures (there is actually a nice story behind SCHNAaP/SCHNArP and the joint Sheffield-Cambridge JMB publications).

In 3DNA, the analyze/rebuild pair of programs is derived directly from SCHNAaP/SCHNArP by using exactly the same CEHS algorithm, with, of course, a change in reference frame, and many added functionalities. Looking back, SCHNAaP/SCHNArP was the starting point leading to later on resolving the discrepancies among nucleic acid conformational analyses, establishing the standard base reference frame by the community, and creating the 3DNA software package that has gained great popularity in recent years.

Since Rutgers has imposed a policy of not-releasing 3DNA source code, allowing access to the original SCHNAaP/SCHNArP code in C would make it possible for others to verify and build on my previous work. As a matter of fact, this section has been created primarily in response to a recent post in the forum. It is more than ten years since the last time I touched the SCHNAaP/SCHNArP C code. For this release, I have only tidied-up the code slightly just to get rid of warning messages from modern gcc compiler.

The package with ANSI C source code can be downloaded from the 3DNA download page [updated 2012-02-28]. If you notice any bugs or have any comments, please post them here to share with the community.

Xiang-Jun Lu

PS. As a side note, Prof. Chris Calladine was the external examiner of my PhD thesis. I communicated with him following 3DNA Nature Protocols publication in 2008, partially because recipe #2 (Figure 3) reproduces roll-introduced DNA curvature initially formulated by Calladine and Drew. It is a pleasure to receive the following comments from him:

I am pleased to know that our simple picture of curved DNA is still instructive !! I am very impressed by your 3DNA software: you have brought things a long way since El Hassan's time, and your work is a fine achievement.

Over the years, my research on nucleic acid structure has been most heavily influenced and inspired by Dr. Calldaine's work: from CEHS to the Zp parameter, and the Calladine-Drew style rectangular base and base-pair schematic representations. They are everywhere in the two 3DNA publications (2003 NAR and 2008 NP). I read it through 3 times (early versions) of the book "Understanding DNA: The Molecule and How it Works" and worked out the exercises. For one thing, I could not find a single mistake (even a typo) in the book, which is such a rare case in this high-throughput era where it won't take much effort to notice obvious errors of various kinds. Needless to say, I would highly recommend this book to anyone who is serious about DNA structures.

9

Site announcements / 3DNA Nature Protocols Paper [vol.3, no.7 (2008), 1213-1227]

« on: September 27, 2008, 12:49:36 am »

As you may already know, a new paper on 3DNA was published in the July 3, 2008 issue of Nature Protocols (NP). Even though this publication has been referred to a few times in the forum, especially in the post by Tomas, I have recently been too busy to  make a formal announcement here. Now, I feel it is the time to get the message out.

First of all, we appreciate your contributions:

We are grateful ... to the users of 3DNA for using the software to address real-world problems, and communicating the difficulties that they encounter. Positive interactions with the users have been the driving force behind the development and improvement of 3DNA.

Following the editor's suggestion, I would encourage you to post your comments and questions related to the protocols paper in the NP website: it is a more prominent and permanent place than the 3DNA forum. You are welcome, of course, to post any 3DNA-related questions in this forum.

In this paper, I selected seven representative examples to illustrate the versatile capabilities made possible only by 3DNA's integrated approach that combines structural analysis, rebuilding and visualization (see the composite image below). Hopefully, I have convinced you that 3DNA is not just for DNA as suggested on the nuccyl website (see also http://xiang-jun.blogspot.com/2009/07/does-3dna-work-for-rna.html), or only for structural analysis (as Curves etc). Importantly, in the NP_Recipes subdirectory distributed with 3DNA v2.0,  I have included all scripts, original data files and generated images, so that qualified researchers should be able to reproduce accurately our results without difficulty. Of course, I am more than willing and would be quick to address any reproducibility issues you may have. Repeatability is one of the basic requirements of a published scientific work, yet in this "high-throughput" / "big science" age reproducibility is sort of becoming a luxury.

Over the years, it has also become quite clear to me that 3DNA is still (heavily) underused, especially with regard to its visualization capabilities, and analysis functionality for RNA structures. Moreover, and most importantly, 3DNA can be refined, extended, and tailored to new applications. I am especially interested in forging serious collaborations with those having real insights in structural biology, willing to share and being responsive: with complementary expertises, some mutual interests and a commitment to excellence, we can have fun together in solving challenging problems in biological (especially RNA) structures.

Xiang-Jun Lu

Cleaned up links on 2012-02-28

10

Site announcements / Activating your newly registered 3DNA forum account

« on: May 03, 2008, 07:43:35 pm »

You do not need to register if you just want to browse through this forum. The content is publicly viewable; no email is sent from this forum.

The moderated-registration policy is enforced to avoid spams on the forum. You should follow the simple rules specified below in order to activate your newly registered account. Otherwise, your 3DNA forum registration will  not be activated -- it will be deleted automatically after a certain amount of time.

[hr:qv3aywkc][/hr:qv3aywkc]
Send an email request to 3dna.lu@gmail.com:

• Use your registration email
• Put your registration ID in the subject line, following the format of Re: 3DNA forum registration -- [red:qv3aywkc]user-id[/red:qv3aywkc][/u]. For example, if your registered id is [red:qv3aywkc]qwerty[/red:qv3aywkc], then the subject line should read: Re: 3DNA forum registration -- [red:qv3aywkc]qwerty[/red:qv3aywkc][/u]

[hr:qv3aywkc][/hr:qv3aywkc]
Thanks for your cooperation.

Xiang-Jun, the 3DNA forum administrator

11

Site announcements / Happy New Year Greeting Pictures from Dr. Pascal Auffinger

« on: January 12, 2008, 12:02:26 am »

Over the past couple of years, I am thrilled to receive (Chinese) new year greeting pictures from Dr. Pascal Auffinger (IBMC-CNRS, France),  one of my respected scientists in the field of nucleic acid structures.

I have communicated with Pascal a lot via email and this forum on 3DNA-related questions that are relevant to his research over the years. I am glad to find that 3DNA has turned out to be a useful tool in his SwS, a Solvation web Service for nucleic acids. During the process, Pascal has helped me in refining 3DNA to make it more robust, and in adding new functionalities.

Positive and responsive interactions with users like Pascal are what drives 3DNA forward.

Thanks, Pascal!

Xiang-Jun

12

Site announcements / Forum updated to phpBB3

« on: January 05, 2008, 11:47:04 am »

Over the past few months, the 3DNA forum has had increased spam-registrations. Luckily, due to the fact that new accounts must be activated by the administrator, no junk posts have appeared in the forum.

While the large number of registrations on the front page of the 3DNA forum looks great, a majority of them constitute spam. When I tried to eliminate these junk accounts, I made a silly mistake...  :oops: and rendered the forum non-functional for a while. As a consequence, a few recent active user accounts and posts are also gone!

To solve the problems from bottom up, I have decided to switch the forum from phpBB version 2.x to the latest of version 3.x. In addition to increased security measures and easier maintenance, the new version has a built-in attachment module. I am also planning to put more material (e.g., online documentation, working examples, etc.) onto this forum. As always, I welcome user feedback and active involvement.  :wink:

Xiang-Jun

13

Site announcements / Add attachments to your post

« on: June 15, 2007, 10:28:15 pm »

From my experience, the most effective way to solve a 3DNA related problem is by checking a minimal reproducible example. I have thus installed the popular phpBB2 Attachment Mod in this forum so that you can directly add attachments to your post.

In case you would like not to make your data public, you can use this simple PHP based file uploader at URL:
http://3dna.rutgers.edu:8080/upload/. Then in your forum post, please mention the name of the file you've uploaded into the server.

Please do make use of these facilities instead of sending me email attachments.

Thanks for your cooperation!

Xiang-Jun

14

Site announcements / Welcome message from Xiang-Jun Lu

« on: March 23, 2007, 02:04:36 am »

Over the past few years, I have been answering hundreds of 3DNA-related questions via email. While this method is effective and convenient, the Q&As are scattered in different email accounts and mixed with other messages, making it difficult to trace the previous thread(s) of a relevant topic. This forum was created to address this issue by making these Q&As open to the community, archived and searchable. To start with, we would like to ensure that this forum is focused on 3DNA related issues. As a general rule, please post your questions here instead of sending me emails: this will benefit the whole community! Only under very special circumstances will I answer your questions directly by email.

This forum is open to the public for viewing without preregistration. You are invited and strongly encouraged to register in order to get more actively involved (by asking questions, following-up other ones, reporting bugs, or making comments/suggestions). Because of spam concerns (yes, I would like to keep the noise level in this discussion forum to a minimum), registrations must be activated by the administrator. Following your registration, please send a message to 3dna.lu AT gmail DOT com from your registered email address and with your user ID in the subject line, following the format of Re: 3DNA forum registration -- 'user-id'. You might also want to share with us some background info about yourself and how you came to know about 3DNA and this website. After receiving your email request,  I will activate your account and send you a confirmation email. -- no longer relevant [note added by Xiang-Jun Lu on Feb 24, 2012]

When asking questions, please be as specific as possible. I have learned through experience that having a minimal reproducible example is the most effective way for me to solve a problem. For general guidelines, please refer to "How To Ask Questions The Smart Way?" To make the 3DNA forum a more pleasant place, please be considerate and practice good netiquette. Most importantly, give, don't just take: summarize the solution to your problems from a user's prospective by providing details for the benefit of other users; answer other users' questions; share your use-cases or anything relevant to 3DNA. More enthusiastic members are essential in making the 3DNA forum more active and informative to serve as a helpful virtual community for each of us to exchange views, to learn and to help.

Bear in mind that I am supporting this 3DNA forum strictly in my spare time: do not ask for or expect to get an immediate reply from me to your question. [-- now supporting 3DNA is my job! note added by Xiang-Jun Lu on Feb 24, 2012] Over the years, however, I have always striven to be responsive and concrete by getting back to users' questions as quickly as possible, often in a step-by-step recipe fashion, with follow-ups until the issue is finally resolved. Hopefully, browsing the forum will convince you that I am well up to this claim  .

So, welcome to the 3DNA discussion forum! Your feedback helps us kaizen (improve; 改善) 3DNA to make it serve the nucleic acid structure community better.

Xiang-Jun Lu (律祥俊）  (so glad to be of help!)

15

General discussions (Q&As) / Welcome to the 3DNA forum

« on: August 17, 2006, 09:53:49 pm »

Over the past few years, we have been answering 3DNA-related questions via emails. While effective and convenient, the information is not archived nor searchable.

This forum is created to address this issue. To start with, we would like to ensure that this forum is focused on 3DNA related issues. Please post your questions here instead of sending us emails.

Welcome to the 3DNA forum, and we appreciate your participation!

Xiang-Jun