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It [DSSR] looks like a combined version of find_pair and analyze. Is that correct ?Yes, to certain extent, you can think DSSR as a combination of find_pair and analyze. The post "DSSR, what's it and why bother? (http://x3dna.org/highlights/dssr-what-s-it-and-why-bother)" provides more background information. You are right, DSSR does not construct nucleic acid structures.
Of course it seems not possible to (re)construct NA structures with DSSR.
So first, why calling it DSSR and not DSSNA since it works also for DNA ?Again, read carefully the post "DSSR, what's it and why bother? (http://x3dna.org/highlights/dssr-what-s-it-and-why-bother)" for my rationale. You may also notice that I put the word secondary in parenthesis in the title of the software, "DSSR: Software for Defining the (Secondary) Structures of RNA". DSSR surely works for DNA, or DNA-protein complexes in the same way as it does for RNA. As mentioned in the release note, I tested DSSR against every nucleic-acid-containing structure in the PDB. Overall, the acronym DSSR captures the essential message I'd like to get across, it is short, and it parallels the well-respected DSSP program for proteins (among other things).
I think that one should avoid the RNA domination, it is possible to learn from both structures.
thus, does DSSR really work for DNA ?
Then, as for formats,
I think that as I mentioned it somewhere earlier, and since I am processing the output files
for a large number of structures, I appreciate when there are spacesbetween fields (see).
base_id alpha beta gamma delta epsilon zeta e-z chi phase-angle sugar-type Zp Dp
1 A.C2649 --- 167.1 47.6 84.1 -146.6 -77.1 -69(BI) -160.5(anti) 12.9(C3'-endo) ~C3'-endo 4.41 4.66
2 A.U2650 -64.2 164.2 60.3 79.8 -154.5 -73.1 -81(BI) -167.2(anti) 21.3(C3'-endo) ~C3'-endo 4.40 4.55I see your point, but the purpose of the output file is mainly for visual examination by a non-expert user. The message appears to be succinct. Your parser should be flexible enough to handle the case. Also see my reply to your initial thread (http://forum.x3dna.org/rna-structures/list-nucleotidenucleotide-contacts-involving-a-phosphate-group/msg1249/#msg1249).and is there a need for writing twice the sugar pucker in this file ?From my experience, the phase angle and pucker classification are the most useful information for the sugar moiety. I repeated the sugar pucker together with commonly used backbone parameters for convenience; one can now easily see the backbone conformation at a glance.
you name this file torsion although there are sugar puckers in it.I see your point, but the file also contains Zp and Dp, and pseudo torsion angles. I'd keep the name as is; it is just a convention to get used to.
Thus it might be called torsion_puckers.dat or something else.
For the non-pairing interactions that is just a great feature,DSSR checks base-stacking interaction using all base atoms, and so is the output value of base-overlap-area. I will consider to add overlap areas based on just ring atoms.
you had before two values for base overlap
one calculated by just using ring atoms the other by using all base atoms.
you could add this.
Why adding the name of the chemical groups (hydroxyl, amino, imino, ...)I added the names of chemical groups (hydroxyl/amino/imino) for the convenience of those who are not that familiar with the chemistry of H-bond. I've first-hand experience with such people (mostly physics/mathematics/computer science turned bioinformaticians). I can add an option to turn the chemical group off; but honestly, I really think you should revised your parser to handle it properly.
again this complicates reading since some groups are named and others not like OP2 and so on.
I would appreciate another presentation here.
H-bonds[2]: "N3(imino)-N1[2.81]; O4(carbonyl)-N6(amino)[3.13]"if your parser can extract the distance and the PDB atom names, it won't be that far to check for () and get rid of the name of the chemical groups.I haven't really checked, but are your base pair numbering scheme coherent with the oneWhat do you mean by "base pair numbering scheme"? The serial numbers should not matter; the base pair is specified by the two constituent nucleotides (chain id, residue name and number, etc).
you use in find_pair ? It would be really nice to be the case.
Also, I wanted to ask you that but know it seems to be done. You add various namesAdvice taken :) -- I will add a note in DSSR-beta-r10 (coming soon).
to each base pair. Thats great. Just a hint to the various nomenclatures (Leontis-Westhof, Saenger...)
would be helpful in the *.out files.
is there a configuration file that would allow to precise hydrogen bond and other parameters like in 3DNA.To make DSSR self-contained, I've eliminated the configuration file. Overall, DSSR has refined algorithms for finding H-bonds, base pairs, helices etc, and the defaults should work for the vast majority of cases. So regular users could take DSSR as a black box, and they can check the results based on their domain knowledge and application needs.
I would really appreciate that.
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