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Miscellaneous items > FAQs
How do I build nucleic acid structures with sugar-phosphate backbone?
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xiangjun:
The easiest way to build a nucleic acid structure with the sugar-phosphate backbone, other than predefined fiber models, is to use the rebuild program. The backbone building scheme uses exactly the same protocol as the default for base-only model. The user needs to add the -atomic option to rebuild, and to choose the desired rigid sugar-phosphate backbone to be attached to the standard base geometry.
The four types of currently available backbone conformations are listed in the directory $X3DNA/config/atomic. To use any of these backbones, it is necessary to copy the standard nucleotide files associated with each type of backbone to $X3DNA/config or your current working directory, and to name each nucleotide as follows: Atomic_X.pdb (where X = A, C, G, T, U; or Atomic.x.pdb where x = a, c, g, t, u for modified bases). The default Atomic_X.pdb files contains only the C1' backbone atom, and the base geometry is independent of the backbone conformation.
To build a DNA structure with B-DNA backbone conformation, for example, one uses the BDNA_X.pdb set to replace Atomic_X.pdb. There is a sub-command cp_std of the Ruby utility program x3dna_utils to help with this: x3dna_utils cp_std BDNA. This will copy BDNA_X.pdb to the current working directory and rename it Atomic_X.pdb. Please note that rebuild searches for Atomic_X.pdb files first in the current working directory, and then in $X3DNA/config.
To make the above description clear, here is an example. Go to the directory $X3DNA/examples/analyze_rebuild, and try to reproduce the following:
* use the command, x3dna_utils cp_std BDNA, so that you will have Atomic_X.pdb files
* use find_pair bdl084.pdb | analyze, to analyze the structure bdl084 (355d) and to generate a file named bp_step.par
* use rebuild -atomic bp_step.par bdl084_3dna.pdb, to generate the PDB file bdl084_3dna.pdb with a standard B-backboneThe RMSD between all atoms of the original bdl084.pdb file and the generated bdl084_3dna.pdb file is only 0.73 Å. Please note that in the rebuilt bdl084_3dna.pdb file, some O3'(i-1) to P(i) linkages can be quite long (broken). This structure, however, serves well as a starting point for further energy minimization. See post "Restraint optimization of DNA backbone geometry using PHENIX" for how to regularize the overlong bonds.
ry54451:
In this process, you generate the parameter file with two header lines.
I understand what the 1st line means.
What does the value associated with the 2nd line mean? I see that it is '0' , but why have it? What does it signify?
Thank you.
xiangjun:
There are actually three header lines, as below:
--- Code: Bash --- 12 # base-pairs 0 # ***local base-pair & step parameters***# Shear Stretch Stagger Buckle Prop-Tw Opening Shift Slide Rise Tilt Roll Twist
The '0' in the second line means this parameter file is using local base-pair and step parameters, as detailed in the third line. This file is named 'bp_step.par' from the output of the 3DNA analyze program.
A parallel output file from the 3DNA analyze program, named 'bp_helical.par', has the following header lines:
--- Code: Bash --- 12 # base-pairs 1 # ***local base-pair & helical parameters***# Shear Stretch Stagger Buckle Prop-Tw Opening X-disp Y-disp h-Rise Incl. Tip h-Twist
Hopy this clarifies the matter.
Xiang-Jun
Shreya Ghosh:
I generated a proper .par file but I was not able to generate a proper pdb file. My pdb file only contains the DNA bases without the P, C5', C4' and other backbone atoms.
How can I amend the error?
Thank you.
xiangjun:
Please provide details. Reproducibility is the key.
Xiang-Jun
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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.
