Topics

1

General discussions (Q&As) / Top view of DNA

« on: May 18, 2017, 06:13:34 am »

Hi

I want to get the top view and side view of a DNA structure.
I got it from stack2img command.
It works well for a pdb i downloaded from PDB database.

When i do it for a pdb i extracted from my trajectory analysis i get only a side view (not the normal side view). The view i am obtaining for the top view and the side are the same ; the one i could see if i open it in any visualization software. The pdb has modofied residues ; but its ok (since the modification is taken care of) and the pdb works well with findpair and analysis commands.

So what must be the problem ; the top and side view option are not working on my pdb


thanking you

mary

2

General discussions (Q&As) / Sugar puckering algorithm in 3DNA

« on: February 01, 2017, 01:46:25 am »

Sir

i would like to know which algorithm is used in calculating sugar puckers in 3DNA to understand the comparison between values obtained from other softwares.


mary

3

General discussions (Q&As) / minor and major grooves

« on: August 17, 2016, 03:10:53 am »

Sir,

i have been using 3DNA for helical parameter calculations.
I have attached 3DNA o/p of two RNA duplexes and a Nucleic acid research paper providing the minor and major grooves of these duplexes (calculated using curves) and standard values of RNA (minor groove 11.0 and major groove 2.7 angstroms) . I would like know your opinion in this matter



standard values are more comparable to curves values.
I need to use 3DNA only as i have modified nucleobased  duplex  and it works with 3DNA.
But i am facing problems when i have to compare with standard values and crystal structures (like 1RNA, !SDR etc)

hoping you valuable suggestions

thanking you

mary

4

MD simulations / base overlap

« on: July 25, 2015, 03:55:43 am »

Sir,

is there any way i could extract the stacked base overlap area as a function of time?
could i extract overlap area in analysis o/p

5

General discussions (Q&As) / base stacking

« on: July 10, 2015, 05:40:19 am »

sir,

Does any helical parameter is directly related to base stacking so that we can a give an account of relative base stacking strength other than visual observation with mstacking or base overlap?

6

General discussions (Q&As) / helical parameters

« on: September 04, 2014, 01:23:55 am »

Sir,

i would like to know which parameter should be changed to increase the width (C1'-C1'  or P-P) of the dna structure. is any helical parameter dependent on width of the double helix?

7

General discussions (Q&As) / minor groove direct measurement

« on: April 23, 2014, 05:00:23 am »

Sir

I would like to know the concept behind measurement of minor groove so that i could directly measure the minor groove (P-P) distance. I mean from which residue no: residue no.  Its surely not a 1-1 measurement; there is some  i: i+r correspondance.
Also in the output file of 'analyze' only 5 minor groove values -> 3 refined minor groove values are given. are there only these values. in the case of ligand binding studies i would like to direclty measure all the possible values. It would be helpful if you could help me in this.

Thanking you.

8

General discussions (Q&As) / std_base

« on: March 13, 2014, 03:18:42 am »

Sir,
I tried the std_base -fit option with xdna as in a earlier post. I tried the same with another modification. It works for A and G but not with C and T modification. I am attaching herewith C modification. I tried changing n2 to n1 ; but doesnt work.  Please look through what goes wrong.

Thanking you

9

General discussions (Q&As) / hybrid analysis

« on: September 09, 2013, 10:31:41 am »

Hi,

On analyzing a RNA/DNA hybrid (RNA--- A/U/G/C and DNA----DA/DT/DG/DC), does x3dna recognizes its a hybrid stucture? Should i give a different designation for RNA strand bases?

Mary Varughese