Hi Gengshi,
Thanks for using DSSR and for posting your well-formulated question on the 3DNA Forum.
Could you please advise whether this tilt is expected due to reconstruction? Or is there a recommended way to maintain the original axis alignment during rebuilding?
Yes, the rebuilt structure and the original structure are in different coordinate systems, as expected. More specifically, the rebuilt structure is in the reference frame of the first base pair, while the original structure is in a whatever coordinate system it was originally in. For the fiber models from 3DNA/DSSR, base pairs grow from top to bottom, with decreasing z-coordinates. You can easily see this by looking at the
dssr-B-DNA-A36.pdb file.
To put the two structures in the same coordinate system, you can use the
--frame option of DSSR. Using your example, the command would be:
# dssr-B-DNA-A36.pdb is the coordinate file from DSSR fiber model
x3dna-dssr -i=dssr-B-DNA-A36.pdb --frame=A.1:wc -o=expt-ref1.pdb
Now
expt-ref1.pdb and the rebuilt structure
dssr-B-DNA-A36-rb10.5.pdb would be in the same coordinate system. This is the simplest way to align the two structures. See the
DSSR User Manual for more details.
It is also possible to transform the rebuild structure into the coordinate system of the original structure. It is a bit more complicated. I will consider write a blog post on this topic in the future.
You can easily verify that rebuild structure and the original structure are indeed very similar in two ways: One way is to re-analyze the rebuilt structure with DSSR, you will see that the base-pair parameters are very close to the ones for the original structure. The other way is perform a superimposition of the two structures, and you will see that the RMSD for the
base atoms is close to 0. See the commands below:
# extract base atoms from the original structure
x3dna-dssr -i=dssr-B-DNA-A36.pdb --select-base -o=exp-base.pdb
# extract base atoms from the rebuilt structure
x3dna-dssr -i=dssr-B-DNA-A36-rb10.5.pdb --select-base -o=rebuild-base.pdb
# the RMSD between exp-base.pdb and rebuild-base.pdb is 0.016.For your verification, exp-base.pdb and rebuild-base.pdb are attached to this post.
While we're at it, here's an excerpt worth taking from the
DSSR User Manual (
5.3 Customized structures):
The 3DNA rebuild program complements analyze by reinforcing and verifying it. These two programs are a defining feature of 3DNA (Lu and Olson, 2003, 2008; Li et al., 2019). The 3DNA analyze and rebuild programs are based on SCHNAaP/SCHNArP (Lu et al., 1997a,b) which implement and extend the rigorous CEHS algorithm (El Hassan and Calladine, 1995) for the analysis/rebuilding of DNA duplexes.
The reversibility of the analysis/rebuilding programs in 3DNA allows scientists to ask what-if questions. By first deriving a complete set of base-pair parameters from an experimental structure, they can then systematically introduce changes in these parameters to see what happens to the shapes of the resulting 3D structures. This is a simple, yet powerful concept. 3DNA is the only widely used DNA/RNA structural bioinformatics tool with this feature. It has led to the discovery of a novel roll-and-slide mechanism to account for DNA folding in chromatin (Tolstorukov et al., 2007). Using modeling studies enabled by 3DNA, the Johnson lab at UCLA has revealed slide as a key parameter (along with roll and twist) in mediating DNA minor groove width (Hancock et al., 2019; Chen et al., 2018; Hancock et al., 2016, 2013; Stella et al., 2010).
The DSSR analyze module has completely surpassed the 3DNA analyze program (see Section 3.18). Similarly, the rebuild module in DSSR replaces the 3DNA rebuild program, with enriched functionality and improved usability. The module must be run as x3dna-dssr rebuild, just like a sub-command in Git.
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