Messages

1

General discussions (Q&As) / Re: Who get 3DNA version 2.0

« on: October 22, 2009, 03:35:06 am »

Hi,

I also had this problem. I received information to download the beta version.
The new website is online http://https://adna.rutgers.edu/, here you can register and download the new version.

Regards,
Ramon

2

General discussions (Q&As) / Re: how the cartesian coordinates transform to PDB format

« on: April 22, 2009, 11:35:18 am »

Attached you'll find the scripts I mentioned.
When you untar, i.e. tar -xvzf pythonscripts.tar.gz
you will get two scripts:
3dna2xplor.py
xplor2pdb.py

To convert a file from 3dna to xplor compatible format, type in the command line:
python 3dna2xplor.py
(Answer the questions it poses, and it will work. I don't know how it handles Thymidine residues)

Then you edit xplor2pdb.
line 8 gives the inputfile. (note: pdbbestand is dutch for pdb file)
line 9 gives the outputfile (This is the one to be written in TRUE PDB FORMAT)
Sorry for this confusing naming of variables.
During my Ph.D. I've written a dozen of scripts, and their not all as neat as they should be.

After editing the file, save and run from the command line:
python xplor2pdb.

In the output file the 'END' at the end of the PDB file has an empty space before it. This should be removed for submission.


Regards,
Ramon

3

General discussions (Q&As) / Re: how the cartesian coordinates transform to PDB format

« on: April 22, 2009, 05:05:14 am »

Hi Si-Ya,

Looking at the reply from Xiang-Jun, I must have misunderstood your question.
I understood your question as how to implement transformation from helix parameter frame to cartesian coordinates.
This is described in the papers:

M.S. Babcock, E.P.D. Pednault, W.K. Olson (1994): J.Mol.Biol., 237(1), pp. 125-156
     -  Formal and correct, but takes some time to read

M.S. Babcock, E.P.D. Pednault, W.K. Olson (1995): J.Mol.Biol., 251(5), pp. 648-664
     -  Easily accessible, but some details are taken from the article I mentioned above

Now I understand you do use 3DNA for this task, but want to transform the 3DNA coordinate file to a proper PDB format.
In the past I have written scripts to convert 3DNA to a format that Xplor (Structure calculation program) can use.
Later I have written a script to convert from X-plor format to PDB format (which is accepted for submitting structures to the online protein databank).
Do you want to submit your structure to the online databank ? Or do you want to do further analysis requiring cartesian coordinates ?

But I think trying Openbabel is certainly worth a try, this is the easiest optin available. It can be obtained in some Linux distributions via the automatic update option (In Fedora Core 9+ as root: yum install openbabel). Otherwise it can be obtained via http://openbabel.org/wiki/Main_Page.

I will look up these scripts (as soon as I booted into Linux again), and post them here. (Or if I have time, combine the two to one 3DNA2PDB script)

Regards,
Ramon van der Werf

4

General discussions (Q&As) / 3DNA version 2.0

« on: April 20, 2009, 06:28:56 am »

Hi,

I've read about version 2.0 of 3DNA. (The website works really nice)
This raises some questions:

1. I sent an E-mail to prof.dr. Olson, but I never get a reply, yet I still would like to use 3DNA v2.0 in the future. Help ?
2. What's new in v2.0 ?
      Perhaps this can be added to the topic on 3DNA v2.0

Regards,
Ramon van der Werf
Ph.D. Student at the Radboud University of Nijmegen, The Netherlands

5

General discussions (Q&As) / Re: how the cartesian coordinates transform to PDB format

« on: April 20, 2009, 06:25:05 am »

Hi Si-Ya,

In the manual of 3DNA, the calculation going from atomic coordinates to helix parameter frame is discussed quite thoroughly.
Further there are some references, which discuss this in more detail. Since I don't have the manual lying around here.....
There is a paper by Babcock et al.. which discusses a couple of parameters, and than there is a paper by Calladine et al (I think), which has quite a "simple" approach for some of the helix parameters.
Sorry I cannot be more specific. If I have the time, I'll look up the references and write them down here.

Unfortunately, it is not a type-and-go solution.
If you have analytical expressions for these transformations, I'd be happy to hear them.

Kind regards,
Ramon van der Werf
Radboud University Nijmegen, The Netherlands

6

General discussions (Q&As) / Re: Rebuilding protonated RNAs with non-canonical basepairs

« on: July 31, 2008, 12:23:40 pm »

Dear Xiang-Ju (and other readers),

Thanks....
I have to read the FAQ... sorry I forgot.

Solution to this problem.
If an A-T basepair is replaced by a U-U basepair in bp_helical.par, the distance between the atoms in the H-bond is too large.

The solution was to be found in FAQ#6, and is the following....
In the X3DNA/BASEPARS/misc_3dna.par

there is a line:

4.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location

I increased the upper H-bond length t0 5.0. So this line looks in my file:

5.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location

Now the basepair is detected, and the problem is solved.

Kind regards,
Ramon

7

General discussions (Q&As) / Re: Rebuilding protonated RNAs with non-canonical basepairs

« on: July 28, 2008, 10:21:13 am »

Dear Xiang-Ju,

Sorry, I mis-formulated... I meant:
I can rebuild a U-U basepair, but analyzing does not work.

Attached is the bp_helical.par file, from which I rebuilt the structure RNA.pdb (protonated).
If subsequently I type:
find_pair rna.pdb stdout|analyze, the bp_helical.par does not contain the U-U basepair.

If you want to, I can tar all Atomic_*.pdb files I use together with the bp_helical.par and so on.

Kind regards,
Ramon

8

General discussions (Q&As) / Rebuilding protonated RNAs with non-canonical basepairs

« on: July 23, 2008, 07:50:16 am »

Hi all,

I am using 3DNA to rebuild RNA helices which are protonated.
To do so, I first build a DNA helix:
fiber -a pdbfile.pdb
subsequently analyze:
find_pair pdbfile.pdb stdout|analyze
Then replace in the parameter files the thymidines by Urdines, and subsequently rebuild using protonated nucleotides to do so.
[Probably there is a fastre way to do so]

My question is the following:
I found 3DNA can handle all basepairs (canonical and non-canonical), the one flaw I discovered is that it cannot handle U-U basepairs.
Can I fix this problem by modifying some file(s) ? Or is it hard-coded into 3DNA ?

Kind regards,
Ramon van der Werf

9

General discussions (Q&As) / Multiple global helical axes in one structure, how to calc?

« on: June 25, 2008, 03:51:40 am »

Hi,

I have a single structure consisting of two helices seperated by some sort of hinge.
The problem is to find the angle between the two helices.
If I look at the [pdbname].out file, which results from
find_pair [pdbname].pdb stdout|analyze
There is not gobal helix axis defined.

What I want is four HETATM lines in the outputfile, defining the begining and the ending of the global helix axis for both helices.
Can I only obtain this by cutting the PDB in parts and then analyze these parts seperately, and append the HETATM lines to the original PDB file ?


Greetings,
Ramon

E.G. structure looks like this (very schematically):


 |--|
 |--| Helix I
 |--|
 /  
 |   | Non-helical hing-area
   /
 |--|
 |--| Helix II
 |--|

I want the angle between helix I and II