Messages

1

General discussions (Q&As) / Re: rebuilding using Modified bases

« on: March 17, 2016, 01:34:52 pm »

Hi 
Thanks for the quick reply.
One way to do will be as u suggested.
But I also want to modify backbone atoms.
I got the answer from your earlier post.

http://forum.x3dna.org/faqs/how-do-i-build-nucleic-acid-structures-with-sugar-phosphate-backbone/msg784/#msg784
Thanks once again,

Best,
kailsen

2

General discussions (Q&As) / rebuilding using Modified bases

« on: March 17, 2016, 01:07:12 pm »

Hi ,

I'm  using rebuild option for regenerating my sequence.
I wanted to change the nucleotide (base+sugar+backbone) coordinates used to a modified nucleotide.
So as to regenerate a new duplex. Which library file used by rebuild module?

Best,
Kailsen

3

RNA structures (DSSR) / Re: Chi torsion definition

« on: November 26, 2015, 04:55:08 pm »

I was referring to the RNA described below.
1R3O.pdb
Crystal structure of the first RNA duplex in L-conformation at 1.9A resolution
DOI: 10.2210/pdb1r3o/pdb

4

RNA structures (DSSR) / Re: Chi torsion definition

« on: November 26, 2015, 03:08:17 pm »

Hi  Xiang-Jun,
Thanks for the quick reply.
I am using 3dna and dssr for Left-handed L-RNA which has L-sugar.  I think logically this should not affect syn/ anti anyway. Correct me if I'm wrong.
Also, I know that most commonly standard D-RNA is used as reference.
Can you comment on the parameters that I have to be careful about considering that fact that the RNA is left-handed L-RNA.

5

RNA structures (DSSR) / Chi torsion definition

« on: November 26, 2015, 01:58:49 pm »

HI ,
I have a doubt on chi angle definition.

My latest version 3DNA has the following definition
          chi in [165, -45(315)] for anti conformation
                 chi in [45, 95] for syn conformation

and DSSR has
  chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4
    Range [170, -50(310)] is assigned to anti, and [50, 90] to syn

The following is an excerpt from ur blog on torsion angle sometime ago.
---------------------------------------------
Normally (as in A- and B-form DNA/RNA duplex), χ falls into the ranges of +90° to +180°; –90° to –180° (or 180° to 270°), corresponding to the anti conformation (Figure below, top). Occasionally, χ has values in the range of –90° to +90°, referring to the syn conformation.
-------------------------------------------

Why is there a difference in the range to define syn and anti?
Why the definition had to be changed compared to the old text definition of ..."+/-90 to +/-180"?

6

RNA structures (DSSR) / What are the definitions of helix, stem, step etc in DSSR?

« on: March 10, 2013, 01:07:27 am »

Hi Lu,
 I have downloaded the DSSR program and above to use it. I will be using to find. pseudo helices. I want to know. what is consideres as an helice? a stem? a step? step has two basepairs. at what level it will be pushed to be called as stem. i see that in ur sample output, the acceptor arm fully will be called helices. am i correct?.

7

General discussions (Q&As) / Re: DNA/ RNA fibre model values

« on: March 02, 2013, 09:51:30 pm »

Thank You so much for the prompt reply

8

General discussions (Q&As) / DNA/ RNA fibre model values

« on: March 01, 2013, 11:03:41 pm »

Dear All,
 I would like to known why in fibre models the values of tilt and shift has to be close to zero. i recently built a RNA model from a webserver  and it had tilt value of 0.5 and shift value of 1.0. then later i was pointed out that the structure was wrong. I confirmed ten by using w3dna for all adna, bdna and arna that the tilt & shift value is close to zero.

9

General discussions (Q&As) / Calculating groove width- calladine algorithm

« on: April 30, 2012, 07:29:29 am »

Hi ,
 I am interested to know the programming part of refined groove width calculation. I read this forum n found abt Calladine paper(1998). In their algorithm it says u fit a curve to three points. What formula was used (as there is more than one way of fitting a curve in 3D space) It will be nice tif u can explain how to go about considerding a example of say thre vectors, V1(x1,y1,z1) ; V2(x2,y2,z2) and V3(x3,y3,z3). Also it will be nice to know of any other algorithm/ work that talks about groove width calculation that is accepted  by Nucleic acid community. their advantages n disadvantages. esp with respected irregular deformed helices.

10

General discussions (Q&As) / Re: NUPARM vs X3DNA twist values

« on: November 13, 2009, 12:58:06 am »

Hi Lu
Thanks for the info.. As  you said, i just had to re-read these earlier papers carefully once again. and understanding the reason was not much of a diff task. Thanx for pointng me in the right direction. BTW, i could nt still CURVES+ program. having problems in running it. Using it for the first time !!!. Asi get the values will post it.

11

General discussions (Q&As) / NUPARM vs X3DNA twist values

« on: November 09, 2009, 10:11:14 pm »

Hi,
 I did some step parameters calculation using 3DNA as well as the NUPARM web server present in the following URL
http://http://nucleix.mbu.iisc.ernet.in/nuparm/nuparm.shtml
The structure is a RNA with GU mismatch in the 4th n 5th steps. The pdb id is 2G3S(attached the coordinate file).
The dinucleotide step contributed by non Watson-Crick base steps alone seems to have different values for Twist (x3dnaTwist=49.67, NUPARM=24.20). On visually examining the step the does not show twist value as high as ~50 degrees. I am aware that the geometric calculation involved in both these programs are different but all other values correlate well including the base step, intrabase step and torsion angles values. Do u think shearing in GU base pair seems to be a reason But, it would be good if u can explain the difference occuring in twist value alone. I have not compared the values with CURVES+ program yet   .Using SCHNAaP/CEHS the twist value is 25.52 which is  close to NUPARM values.

12

General discussions (Q&As) / Re: 3DNA calculation for Bases that have two conformers in pdb

« on: October 10, 2009, 06:15:57 am »

Hi Lu,

 Thanks you for clarifying my doubt. Sorry for the discrepancy in the PDB ID. Pls  see 483d.pdb  instead. I had  removed the ANISOU lines for clarity.

ATOM     27  C4 A  U A2647     -28.663  57.538  -5.049  0.58 17.81           C  
ATOM     28  C4 B  U A2647     -29.492  57.317  -4.727  0.42 18.11           C  
ATOM     29  O4 A  U A2647     -29.141  58.325  -4.234  0.58 16.26           O  
ATOM     30  O4 B  U A2647     -30.281  57.919  -4.000  0.42 18.56           O

13

General discussions (Q&As) / 3DNA calculation for Bases that have two conformers in pdb

« on: October 08, 2009, 12:29:46 am »

Dear Sir,
 I would like to know which of the two bases does 3DNA consider while calculating the parameters in cases where the pdb has two conformers for a single base
e.g from 437D.pdb
ATOM     47  O4'A  G A2648     -26.371  52.168 -12.884  0.58 13.58           O  
ATOM     48  O4'B  G A2648     -25.879  52.221 -11.854  0.42 16.38           O
ATOM     49  C3'A  G A2648     -24.982  50.605 -13.934  0.58 11.81           C  
ATOM     50  C3'B  G A2648     -24.120  50.873 -12.569  0.42 14.39           C

I some cases one of the bases is completely flipped out, while in some the bases overlap each other except for the few atoms. I note this happening mainly in RNA GA base pairs

14

General discussions (Q&As) / mutating DNA in DNA protein complex

« on: October 01, 2007, 12:11:05 pm »

I am a graduate student with biochemistry background. Currently i am working on DNA protein interaction and recently came to know about 3DNA through hundreds of citations that your software has received.
I tried to use the software to understand the effect of DNA mutation on binding of the protein. The Transcription factor in question has the pdb code 1GJI. The DNA sequence in this complex is GGGTTTAAA... and i want to mutate this sequence to GGATAAAAA... Preferably,I want to make the changes in the DNA protein complex itself keeping the backbone same. I hope it will be possible using your software.
Is it advisable to use Rebuild program to get the desired changes incorporated?

thanking you in advance for your help

dnaserver