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Questions and answers => RNA structures (DSSR) => Topic started by: wangshsh on February 24, 2017, 11:56:58 pm

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Title: Questions of calculations of inter-base angles
Post by: wangshsh on February 24, 2017, 11:56:58 pm
Recently, I am trying to use X3DNA to calculate tentatively the inter-base angles in dinucleotide monophosphates. When the two bases are in the nearly canonical state, using the --non-pair option can put out the value of the inter-base angle. However, when the two bases are in a nearly vertical state, using the --non-pair option gives results like these:

Command: x3dna-dssr -i=1.pdb --non-pair -o=1.out
Date and time: Sat Feb 25 12:38:29 2017
File name: 1.pdb
    no. of DNA/RNA chains: 1 [A=1]
    no. of nucleotides:    1
    no. of atoms:          39
    no. of waters:         0
    no. of metals:         0

However, in the 1.pdb (please see the attachment), there are two nucleotides not one! In this case (1.pdb), I want to know whether or not X3DNA can give the value of the inter-base angle. If it can,  how to  set up the command lines? Thanks very much!
Title: Re: Questions of calculations of inter-base angles
Post by: xiangjun on February 25, 2017, 12:31:50 am
In file "1.pdb", the second nucleotide A.DT2 is too distorted that is out of the default cutoff of a planar base. Try to run DSSR with the --nt-cutoff=0.9 with get what you want.

Code: [Select]
# Running the following command:
# x3dna-dssr -i=1.pdb --nt-cutoff=0.9 --non-pair
# You will get the following:

File name: 1.pdb
    no. of DNA/RNA chains: 1 [A=2]
    no. of nucleotides:    2
    no. of atoms:          39
    no. of waters:         0
    no. of metals:         0
    total number of non-pairing interactions: 1

****************************************************************************
List of 1 non-pairing interaction
   1 A.DG1 A.DT2 stacking: 4.0(1.3)--pm(>>,forward) interBase-angle=61 connected min_baseDist=2.25

...
Summary of structural features of 2 nucleotides
  Note: the first five columns are: (1) serial number, (2) one-letter
    shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base
    ring atoms fitted against those in a standard base reference
    frame. The sixth (last) column contains a comma-separated list of
    features whose meanings are mostly self-explanatory, except for:
      turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees
      break: no backbone linkage between O3'(i-1) and P(i)
   1  G . A.DG1 0.019  anti,~C2'-endo,BI,non-pair-contact,ss-non-loop
   2  T . A.DT2 0.850  anti,~C2'-endo,non-pair-contact,ss-non-loop

You may need to pay attention to such unusual cases. Are you running MD simulations?

For your own understanding of the issue and the benefit of other users, please provide an image showing the non-planarity of the second base in your example structure.

Xiang-Jun
Title: Re: Questions of calculations of inter-base angles
Post by: wangshsh on February 25, 2017, 01:35:45 am
Not MD simulations, the nearly vertical state (related picture is given in the attachment) corresponds to the TS state of the addition reaction between G/C8 and T/C5.

The question is addressed, Thanks very much!  :) :) :)

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University