Messages

1

w3DNA -- web interface to 3DNA / w3DNA on Nucleic Acids Research

« on: July 22, 2009, 10:14:23 pm »

Hi all,

A detailed description of the w3DNA (web  3DNA) has been published on the 2009 Web Server Issue of the Nucleic Acids Research journal:

Zheng G., Lu X-J. and Olson W.K. (2009) Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures, Nucleic Acids Research 37(Web Server issue), W240-W246

It is linked to: http://http://nar.oxfordjournals.org/cgi/content/full/37/suppl_2/W240

For technical tutorials, please refer to the w3DNA interface at http://http://w3dna.rutgers.edu


Guohui

2

General discussions (Q&As) / Find DNA-protien contacts using 3DNA

« on: April 16, 2009, 11:12:53 am »

Hi Xiang-Jun,

In your nature protocols paper (Nature Protocols 3, 1213 - 1227 (2008)), you illustrated an automatic generation of structured waters around base pairs and dinucleotide steps in nucleosomal DNA, using the option '-w' with 'find_pair' (Box. 5). Is there a direct option/function to find amino acid atoms around base pairs, i.e. protein contacts with DNA/RNA? Or can you suggest a way to combine various 3DNA functions to approach this?

Thanks.

Guohui Zheng

3

General discussions (Q&As) / 3DNA has a web interface now

« on: April 07, 2009, 03:40:57 pm »

Hi all,

Please refer to the sub-forum of "w3DNA web server topics" (http://http://3dna.rutgers.edu:8080/forum/viewforum.php?f=10). You will find information about our newly-developed web interface for the 3DNA software package. Any regards on the w3DNA server are welcomed to post there.

Best,
Guohui Zheng
Working with Dr. Xiang-Jun Lu and Prof. Wilma K. Olson

4

w3DNA -- web interface to 3DNA / Welcome to w3DNA web server

« on: April 07, 2009, 03:34:03 pm »

Hi all,

We recently developed a user-friendly web-based interface to the 3DNA software package, called w3DNA (http://http://w3dna.rutgers.edu). Our new web-based interface provides straightforward access to some of the most popular features of the 3DNA software, covering Analysis, Rebuilding, and Visualization.

Please visit our web server and test your examples. Any comments or suggestions are welcomed to post here. Your inputs will be valuable to make the server more friendly and robust.

Best,

Guohui Zheng
Working with Dr. Xiang-Jun Lu and Prof. Wilma K. Olson

5

w3DNA -- web interface to 3DNA / analysis outputs

« on: December 28, 2008, 09:26:40 pm »

Hi Xiangjun,

I begin to write documents on the webpage, such as description of output files, tutorials, etc.

Could you please advise which of following output files one would be interested to checking out?


------------------
1WD1.inp  auxiliary.par   bp_order.dat     col_chains.scr   hstacking.pdb
1WD1.out  bestpairs.pdb   bp_step.par      col_helices.scr  ref_frames.dat
1WD1.pdb  bp_helical.par  cf_7methods.par  hel_regions.pdb  stacking.pdb
1WD1.outs
----------------

And could you please write a description for each of the output files, including purpose, description for each column if possible, criteria, etc? I don't really understand all of these. Later on, I will place your descriptions right under the output files on the web and in the tutorial page.

Thanks for your help. It would be nice if you can have them ready as soon as possible.

Guohui

6

w3DNA -- web interface to 3DNA / baselist

« on: December 23, 2008, 07:59:14 am »

Hi Xiangjun,

As you know, unknown bases may be found in a specific pdb, and unknowns should be added to the baselist.dat file in order to let 3DNA process further.

Since I have to pre-analyze all lately updated structures contained by NDB, I must deal with this in an automatic way. What I did is:

1) find_pair XX.pdb XX.inp >& log
2) if file_exists(XX.inp) goto analyze, else fopen(log), find the unknown bases and goto next step.
3) foreach unknow base (triplet), if the first letter matches any of {A, T, C, G, U} , then this bases is represented as the matched base in lower case {a, t, c, g, u}; if no match for the first letter, goto the second, ... up to all the three letters; if no match for all the three letters, the base is replaced by an arbitrary letter 'n'.

I understand that such way is risky, although normally a mutated base contains one and only one wild-type base. What is your suggestion to deal with this? Any knowledge about the naming rule of mutated bases.

Thanks.

Guohui

7

w3DNA -- web interface to 3DNA / NMR analysis

« on: December 23, 2008, 07:43:19 am »

Hi Xiangjun,

Your suggestion of using find_pair -s / -p is very very useful, especially for RNA structures.

After running:
1) find_pair -s 1KX5.pdb 1KX5.inps     --- I will get chain, residue information of each base in order
2) analyze 1KX5.inps     ---I will be able to obtain information of base step parameters

Now, I assume that bases are in the same order in both files of 1KX5.inps and bp_step.par. What I mean here is, the first base in the bp_step.par is the first base listed in the 1KX5.inps, second to second, and so on. By presenting the base step parameters I would need to tell users the associating chain and residue information of each base.

I also have questions for analyzing nmr structures.

1) find_pair/analyze and nmr_strs  both give an output of inp, auxiliary.par, bp_step.par .... , which contain information of only one structure. Now, is this structure the first model of the NMR pdb, or an average structure?

2) Based on your experience, normally how many (range, maximum) models are contained in one deposited nmr pdb file? I found that not many nmr structures provide the whole ensemble on the NDB. Your answer will help me determine the capability of providing outputs regarding all nmr models.

Thanks.

Guohui

8

w3DNA -- web interface to 3DNA / Re: Logo

« on: December 22, 2008, 12:48:35 pm »

Hi Xiangjun,

Can you make a mini-version of the w3DNA_logo you made the other day? That would be used in subpages.
The size could be 50% weight 50% height of the original one.

Thanks.

Guohui

9

w3DNA -- web interface to 3DNA / w3dna web progress

« on: December 22, 2008, 10:59:38 am »

Hi Xiangjun,

You may take a look at the lately updated w3dna web server:

http://w3dna.rutgers.edu

There, some of functions are under building up therefore may not working. But you can review the general framework. And I will be working on writing documents such as About and Tutorial. I would like to invite you to have inputs on this server, such as suggestion, writings for the "About" section, etc.

P.S. Wilma and I are working on writing a proposal letter to the editor, which should be sent out at the end of this month.

Thanks.

Guohui

10

w3DNA -- web interface to 3DNA / web access

« on: December 11, 2008, 07:23:45 pm »

Hi Xiangjun,

As you may remember, we have accessing problem to the X3DNA through the web, namely the apache user doesn't have the permission to read X3DNA parameter files due to the environment set-up.

It was solved by a temporary solution: setting up the X3DNA environment in the command line, e.g.,

env  X3DNA=/usr/local/X3DNA_2.0  /usr/local/X3DNA_2.0/bin/find_pair 1KX3.pdb

However, this method doesn't work when I tried to run the blocview command, since it calls molscript and raster3d, which also have environment or permission problems. So the best way would be setting a local account that can be directed by the apache.

Our computer staff was assisting on this, but he didn't figure out how to configure the server to run through the PHP web as a particular local user. The other day, you memtioned that there is a way to running through the web as a local user. Can you suggest several ways to do so? I will discuss with the computer staff.

Thanks.

Guohui

11

w3DNA -- web interface to 3DNA / Re: Jmol as an alternative for visualization?

« on: December 09, 2008, 02:50:34 pm »

Hi Xiangjun,

I would like to offer various visualization tools, including Jmol, King etc., which I am working on.

Regarding to the fiber model construction, Wilma suggested generate a fiber with combination of different fiber models, such as 5 repeats A form + 5 repeats B form. We understand that the difficulty is the connection of two fiber models (backbones). What do you think of having this option on our web server?

Thanks.

Guohui

12

General discussions (Q&As) / Re: Continuous polymer

« on: December 09, 2008, 01:00:26 pm »

Since you changed the base-pair step parameters and connected repeating crystal structures, you changed the relative association of waters, ions with DNA atoms. It seems that you would need to refine the model by conducting minimization if you want to keep waters and ions with sense. To do this, you may follow:
1) After analysis, express ions and waters onto a specific frame, e.g. the middle base-pair frame. You would need to perform rotations + translations as suggested by Dr. Lu. You will have 4 such frames ( 4 pieces of 8-bp DNA)

2) After rebuilding, analyze again to find the 4 frames that you just used in Step 1.

3) Insert waters and ions relating to each of the reference frames in Step 2. So far, you have a model with 32-bp structure with waters and ions.

Then, you would need to conduct minimization, which I am not very familiar with. But I guess, those X-ray/NMR software will do, such as CNS (Crystallography & NMR System), or maybe Amber will do as well.

HTH.

Guohui Zheng

13

w3DNA -- web interface to 3DNA / Logo

« on: December 08, 2008, 12:35:22 pm »

Hi Xiangjun,

Just to let you know that the web access to the X3DNA (env problem) had been solved. And I made some small progress on the web project:

http://dnaserver.rutgers.edu/~ghzheng/w3dnadev/

There, analyzing a pdb structure with a valid ID is mostly working except for the data grids (check the download section).
As a start, rebuilding a simple fiber functions.
Many of links on the webpage just don't work and still under construction.

Here, I am writing to ask you for designing a logo for our web server. As you see, I made a temporary log on the front page, but I don't think it looks beautiful. You have a lot of experience of creating fancy pictures. Could you please make one or give some idea? Thanks.

And any suggestion on the further development?

Guohui

14

w3DNA -- web interface to 3DNA / Re: Rebuilding part

« on: December 01, 2008, 04:16:46 pm »

Hi Xiangjun,

Thanks for your prompt response.

I did the exact thing as you mentioned. I allow users to type in the sequence (by textarea) or use the repeating unit. Multiple choices are provided to users through a web form.

I did try the indirection '<' before asking you, but I didn't work it out. But now, I got it:

>> fiber -b fiber_b.pdb < par.txt > log

[hr:1jxh7qj1][/hr:1jxh7qj1]
par.txt:

1
seq.txt
[hr:1jxh7qj1][/hr:1jxh7qj1]
seq.txt:

AAACCCGGGTTTAAA
[hr:1jxh7qj1][/hr:1jxh7qj1]

The par.txt file tells the fiber program the input options (line 1: 1 for sequence file), and the sequence file (line 2: seq.txt). It works very well. Thanks.

Guohui

15

w3DNA -- web interface to 3DNA / Rebuilding part

« on: December 01, 2008, 01:26:22 pm »

Hi Xiangjun,

I am working on the Rebuilding part as you suggested:

[hr:oont1n9o][/hr:oont1n9o][li:oont1n9o]Rebuilding: put fiber model-building part first since this is the most-useful part to the general community; add sequence-specific building funcationality next: do not forget with sugar-phosphate backbone in various conformation, and the simplified Calladine-Drew style in Alchemy format. The download page should also be linked to Jmol/RasMol for online view.[/li:oont1n9o][hr:oont1n9o][/hr:oont1n9o]

Now, I have a question here:

For the fiber model-building part, I am trying to use the program "fiber", am I right? This program requires parameter inputs from the screen/keyboard, to provide the sequence information. However, if we want to execute it from the web, this could be a trouble, since we won't be able to type it those information. Is it possible that you can adjust the program a little bit such that all parameters (maybe data files) could be included in just a command line, such as "fiber -s sequence.txt -a fiber_a.pdb"? Or do you have any other ways to solve this? Can I use "rebuild"  function as an alternative? How? Thanks.

Best,
Guohui

16

w3DNA -- web interface to 3DNA / Re: What kind of services we will provide?

« on: December 01, 2008, 11:50:41 am »

Thanks - Xiangjun. I will move on with your advice and let you know any progress.

17

w3DNA -- web interface to 3DNA / What kind of services we will provide?

« on: November 29, 2008, 12:18:52 pm »

Hi Xiangjun,

I created a framework for the web interface, setting up the overall php framework (CodeIgniter framework), Flexigrid grid (Gridview of data), and mysql tables. Currently, as a test, I have a starting page
http://dnaserver.rutgers.edu/~ghzheng/w3dnadev/
There, please just try typing in 1KX3 (no others, others might not work due to the 3dna web access problem, which I am still working with the computer supporters).

Basically, I am asking for your advice. What kinds of services do you think we can provide on either of the three sub pages: Analyzing, Rebuilding, and Visualizing.

1) Analyzing: I am thinking to show results of nucleic acid sequence, base pairing, base-pair parameters, base-pair step parameters.
2) Rebuilding: I am thinking to allow build i) ideal fibers and base-pair steps; ii) DNA/protein complexes with DNA/protein complex templates, i.e. protein coordinates will be integrated into the structure; iii) is it possible to visualize the pdb files in an embedded visualization tool, such as vmd?
3) Visualizing: I am thinking to provide blocview...

There are lots of beautiful functions of 3DNA that I am just not very familiar. Please advise me what kind of services we can provide and attract users.
Thanks.

Guohui

18

General discussions (Q&As) / Re: 3DNA misses one pair of nucleotides

« on: November 01, 2008, 09:53:17 pm »

Can you please make clear what was your problem and how you fixed it? I don't get it.
Thanks.

Guohui

19

General discussions (Q&As) / Re: Unknown residue DC

« on: September 16, 2008, 04:32:59 pm »

Hi,

I would suggest you look through the Q&As, where you should be able to find that this issue has been raised before. This is due to a recent update of pdb format by the Protein Data Bank (as I remember, at the end of last year?). In the new format, bases DA, DT, DC, and DG are specified for DNA, while A, T, C, and G for RNA.

What you can do is:

1. Go the the 3DNA folder at where you installed.
2. Find the subfolder BASEPARS, and get in.
3. Open the file baselist.dat. In the file you will see basically two columns of residue names.
4. At the bottom of the file, add
DA      A
DT      T    
DC      C
DG     G
5. Save the file

Retry find_pair, and you should be fine.

Hope it works!

Guohui Zheng

20

General discussions (Q&As) / Calculate step parameters given two planes

« on: September 21, 2007, 03:39:04 pm »

Hi,

Is there any function of X3DNA that can provide the 6 step parameters between two planes whose origins and orientations are given? For example, we can have a file including such information:

plane #   OX   OY   OZ    Xx   Xy  Xz  Yx  Yy  Yz  Zx  Zy  Zz
plane 1    *      *     *     *     *    *     *    *   *    *    *   *
plane 2    *     *      *     *     *    *     *    *   *    *    *   *

then, 3DNA can tell the step parameters.


Or shall we write own codes to do this, by following the technical algorithms in the 3DNA mannual?

Thanks.

21

General discussions (Q&As) /

« on: August 06, 2007, 12:57:48 pm »

Hi,

Sorry to confuse you. In fact, in PDB, all structures containing DNA polymers, use the new base names. But so far, NDB files still keep using the old format.

For example, check out and compare the part of DNA atoms in following two files:

1) PDB:   http://www.rcsb.org/pdb/files/1kx5.pdb
2) NDB:  ftp://ndbserver.rutgers.edu/NDB/coordin ... /1kx5.pdb1

But you are right, we can consider new names as "unknown bases".

Guohui

22

General discussions (Q&As) / changes of pdb format (A -> DA, T-> DT etc)

« on: August 03, 2007, 10:51:02 am »

Hi Xiangjun,

I found the pdb format was recently changed a little bit in the PDB. For example, in the DNA atom coordinate part, the bases used to be A, T, C, G, but now  they became DA, DT, DC, DG.

So now if we directly run 3DNA for current pdb files downloaded from pdb, it will clash. Can you take into account this change to your next release? Is it OK that if I just change baselist.dat file to add in DA, DT, DC, DG?

Thanks.

23

General discussions (Q&As) / blocview base pairs

« on: July 06, 2007, 11:10:46 am »

blocview can be used to represent each base of DNA as a slabe. I have a normal double-helix B-DNA. Then is it possible to represent each BASE-PAIR as a slabe, rather than each base as a slabe?

What function should I use? and how? Thanks.

24

General discussions (Q&As) / xyz coordinates of O1P atoms

« on: June 29, 2007, 12:21:53 pm »

How can I get the O1P and O2P atoms' coordinates w.r.t the middle frame of each dimer? After doing "find_pair -t *.pdb stdout | analyze", in the auxiliary.par files, we can see xyz coordinates of C1' atoms, xyz coordinates of P atoms w.r.t. the middle frame of each dimer, etc. But there are not datas for, xyz coordinates of O1P atoms w.r.t. the middle frame of each dimer.

I did find_pair after correction of o1p_o2p labeling. Bascially, if I try 1KX5.pdb, which has normal labels of O1P and O2P, I still have trouble to obtain coordinates of O1P and O2P w.r.t the middle frame of each dimer.

Can you let me know how I can obtain the information? Thanks.