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Author Topic: How to detect very distorted base pair?  (Read 483 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/

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* DSSR 2.0 has superseded the 3DNA v2.4 suite

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.

Offline lvelve0901

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Re: How to detect very distorted base pair?
« Reply #3 on: September 13, 2020, 12:31:45 pm »
Dear Xiangjun,

I have two more examples of very distorted base pairs in existing PDB structures that X3DNA-DSSR is not able to detect it. I would like to know the reason and whether there is anyway to adjust the cutoff to be able to detect it?

(1) PDBID: 4NCB nt1: C.DT14 nt2: D.DA6
(2) PDBID: 5LGY nt1: E.DA17 nt2: F.DT5

Thanks.

Best,
Honglue

Offline xiangjun

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Re: How to detect very distorted base pair?
« Reply #4 on: September 13, 2020, 01:34:34 pm »
Hi Honglue,

By default, DSSR does not detect these two base pairs because it fails to identify any H-bond between corresponding bases in each pair. These are the cases where users need pay attention to.

For your own understanding and the benefit of other users, it helps that you create an image for each of these base pairs, marking the distances between presumably H-bonded atoms.

Best regards,

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

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

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.