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Author Topic: How to detect very distorted base pair?  (Read 138 times)

Offline lvelve0901

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How to detect very distorted base pair?
« on: January 20, 2020, 05:09:25 pm »
Dear Xiangjun,

I have a structure of a very distorted G-C base pair (C is modified) see attached. I want to output the base pair parameters like shear, buckle, opening but if I detect the base pair in DSSR it is not in the pair list. Could you please let me know how to analyze such very distorted base pair? Do I need to modify any cutoff?

Thanks.

Best,
Honglue

Offline xiangjun

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Re: How to detect very distorted base pair?
« Reply #1 on: January 20, 2020, 06:55:51 pm »
Running DSSR with the default settings on distorted_bp.pdb

Code: [Select]
x3dna-dssr -i=distorted_bp.pdb --more
I got the following:

Code: [Select]
List of 1 base pair
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 K.DOC13        M.DG6          c-G --          n/a       cWW  cW-W
       [-122.8(anti) .... lambda=75.4] [-98.1(anti) .... lambda=84.4]
       d(C1'-C1')=7.91 d(N1-N9)=7.43 d(C6-C8)=9.40 tor(C1'-N1-N9-C1')=-11.8
       H-bonds[1]: "N4(amino)*N1(imino)[3.56]"
       interBase-angle=11  Simple-bpParams: Shear=-0.50 Stretch=0.34 Buckle=0.5 Propeller=-11.4
       bp-pars: [-0.52   0.30    0.26    1.33    -11.32  51.91]

Isn't that what you're looking for?

Xiang-Jun

Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: How to detect very distorted base pair?
« Reply #2 on: January 20, 2020, 07:03:32 pm »
I see what is going on!

I was using DSSR version v1.6.5-2017jan22 and it failed to detect such base pair.

By using a new version you gave me before v1.9.4-2019jul08, I am able to detect it. Thanks.

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.