Messages

1

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

« on: May 18, 2017, 11:38:09 am »

I will check and come back.

I didn't see anything like that in chimera or pdb.
If I just rotate and position it will be biased.


Thanking you
Mary

2

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

« on: May 18, 2017, 06:51:27 am »

Hi

I am attaching the four files

1. topview_3dna.png   the figure i saw in x3dna tutorial
2.  a dna structure dne_l.pdb
3. topview  dne_l.ps from 3dna  ---> is this figure came out as intended?
4. the modified dna pdb clust1.pdb  ---> i hope its reproducible
5. the figure obtained from 3dna for top view  clust1.ps

Does 3DNA correct the orientation of pdb automatically?


mary

3

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

4

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

« on: February 01, 2017, 11:11:13 am »

Thank you very much sir

5

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

6

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

« on: August 17, 2016, 01:37:55 pm »

ok sir it surely be cited.
thanking you

mary

7

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

« on: August 17, 2016, 01:13:24 pm »

sir,

the component missing was the same nar.jpg attached.

i need to use 3dna only.
but i couldnt compare with the standard A-RNA major groove width which is around 2 angstrom. when standard structures are analyzed with 3dna its around 6 angstroms.

so i dont understand what to do.

also sir i should use P-P refined value. isnt?

thanking you

mary

8

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

9

MD simulations / Re: base overlap

« on: July 26, 2015, 11:39:16 am »

ok sir

10

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

11

General discussions (Q&As) / Re: base stacking

« on: July 14, 2015, 03:03:23 am »

ok sir, i wil try.

12

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?

13

General discussions (Q&As) / Re: helical parameters

« on: September 17, 2014, 02:54:45 am »

sir,

i got it by increasing the stretch as you have suggested.

thank you very much sir

14

General discussions (Q&As) / Re: helical parameters

« on: September 16, 2014, 05:45:36 am »

ok sir, i got the backbone widened. it may suit my requiste

thank you sir

15

General discussions (Q&As) / Re: helical parameters

« on: September 16, 2014, 01:35:55 am »

Sir,

i have a modified nucleic acid with C1'-C1' distance about 13 A. i tried to create its rna counter part by using rebuild and std_base like that. but backbone didnt build up. so i added it using another software, minimized and got backbone linkages (O3'-P) correctly but puckering conformations are not good. so i thought if i could change P position information or i could change a normal rna into larger diameter i could get what i am looking for.

16

General discussions (Q&As) / Re: helical parameters

« on: September 11, 2014, 01:29:01 am »

sir

i want a widened backbone,
C1'-C1' distance ~13 A

Also sir, how could i add custom P position in the Pxyz.dat file? could it help in getting a wide backbone.
Also i dont understand the usage of idx option.

17

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?

18

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

« on: April 25, 2014, 12:59:53 am »

ok sir.
thanking you

mary

19

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

« on: April 24, 2014, 02:48:38 am »

Sir,

I go through the auxillary.par file.
all possible P-P distances are given.
But i would like to know which P-P distance is to be taken (the least distance or is there any particular correspondance like i : i+n)?
I want to understand the difference in the minor groove due to binding of a ligand ; near and away from the region of binding.

Thanking you
Mary

20

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.

21

General discussions (Q&As) / Re: std_base

« on: March 14, 2014, 07:18:55 am »

Sir,
Thank you very much.
I think that's working.
Hope the overall structural parameters would not be affected by this change in atom. The analysis will not be completed without helical parameter; after all other analysis done.

Thank you very much

mary

22

General discussions (Q&As) / Re: std_base

« on: March 14, 2014, 12:36:27 am »

Sir,
So it means i couldnt get analysis of a modified DNA containing such a residue? No trick is possible?
Also
I didnt get NUCPARM . Is it available.? Could nucgen and nucparm can be used to analyze modified residues?

Thanking you for your valuable suggestions,

mary

23

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

24

General discussions (Q&As) / Re: hybrid analysis

« on: September 11, 2013, 08:12:10 am »

thank you very much sir for the paper

25

General discussions (Q&As) / Re: hybrid analysis

« on: September 10, 2013, 07:29:57 pm »

ok sir, i will try DSSR.
i have no access to "2008 3DNA Nature Protocols paper". could you please provide this paper?
Thank you