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Messages - prasun30

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1
General discussions (Q&As) / 3IGK and Tilt value
« on: November 11, 2016, 08:42:28 am »
Dear Forum

I am encountering a peculiar problem while running 3DNA for PDB ID: 3IGK.
Since, it has only single strand, I downloaded the biological assembly and used it.

I am appending the local basepair steps:

Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 GG/CC      0.89     -0.38      3.53      4.20      0.53     33.47
   2 GC/GC     -0.63     -0.31      3.36     -2.73     -0.93     38.79
   3 CA/TG      3.12     -3.38      2.07   -174.43     -5.33    108.92
   4 AT/AT     -1.54     -0.00      3.10     11.53     -0.00    -75.14
   5 TG/CA     -0.07      3.65      3.47     -3.19      4.47      3.50
   6 GC/GC      0.63     -0.31      3.36      2.73     -0.93     38.79
   7 CC/GG     -0.89     -0.38      3.53     -4.20      0.53     33.47
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.      0.22     -0.16      3.20    -23.73     -0.24     25.97
      s.d.      1.53      2.04      0.52     66.68      2.89     54.85
****************************************************************************

Please have a look at tilt value for the serial number 3 CA/TG step.
Can somebody guide me regarding the possible reasoning behind it.

Regards
Prasun

2
General discussions (Q&As) / Re: NUPARM vs 3DNA
« on: October 10, 2015, 08:59:18 am »
Dear Xiang

Definitely I will.

Regards
Prasun

3
General discussions (Q&As) / Re: NUPARM vs 3DNA
« on: October 09, 2015, 02:17:51 pm »
Dear Xiang

Thanx alot for the suggestion. I will try using the command line.

Regards
Prasun

4
General discussions (Q&As) / Re: NUPARM vs 3DNA
« on: October 09, 2015, 01:26:55 pm »
Dear Xiang

Thanx alot for the detailed and prompt reply. It is really helpful to me.
I was wondering if the web server can also give the "auxiliary.par" file (just for the download).
I did not find on the result page (sorry if I have overlooked it).

Regards
Prasun

5
General discussions (Q&As) / NUPARM vs 3DNA
« on: October 09, 2015, 11:19:17 am »
Dear Forum

I was comparing the results of NUPARM with those of 3DNA, especially the inter
strand PP distances (NUPARM) and groove widths (3DNA).

While doing so, I was able to trace the major groove width in the PP distance
matrix, but was unsuccessful in the case of minor groove.

I took 1BNA as a test case. I am attaching the file containing groove widths and
PP distances.

When I calculated the distances between two phosphates using PyMol, NUPARM seems
to be giving correct values. Please let me know, where I am doing something
wrong.

My point is that the P-P distances given by the 3DNA and NUPARM, should be
matching to each other and I should be able to find them in the matrix.

Regards
Prasun Kumar

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.