I recently came across the Direk & Doluca (2024) paper on CIIS‐GQ: Computational Identification and Illustrative Standard for representation of unimolecular G‐Quadruplex secondary structures. Since DSSR is mentioned extensively in this work, with a section comparing CIIS-GQ and DSSR in supplementary materials, it is worthwhile to explore the issues raised in the paper. Overall, following literature allows me to clarify misconceptions and fix bugs that further improve DSSR.
The data which contain the G-quadruplexes were identified by DSSR-G4DB website [12, 13, 16]. All of the PDB (protein data bank) ids of DNA and RNA structures are extracted from the aforementioned website and the pdb files which contain the three dimensional data of the corresponding structures were downloaded from the protein data bank [3–5]. [under section "Materials and Methods": "Data"]
The DNA and RNA structures listed in 3DNA website were identified and downloaded from Protein Data Bank. Only unimolecular structures were used for the rest of the study (Supplementary Fig. 2). [under section "Results"]
Additionally, DSSR requires licensing to get annotation results for G-quadruplex structures. Fortunately, the annotation results for a number of G-quadruplexes were already published at DSSR-G4DB (46) and we were able to compare. [under section "Comparison with DSSR" in supplemental materials]
I am glad the DSSR-G4DB website served as a starting point for this study. The G4.x3dna.org website, where DSSR-G4DB is hosted, has always been available to the public. With the NIH R24GM153869 grant support, the standalone DSSR software is free for academic use and can be obtained from the Columbia Technology Ventures (CTV) website.
All obtained results for each pdb file were compared with DSSR. Out of which 35 DNA and 13 RNA structures were analyzed differently (Supplementary Table 2). Significant differences were detected for a number of structures between CIIS-GQ and DSSR analysis. For example, in 1k8p, 3ibk, 6ip7 and 5ccw structures, DSSR fails to identify some loops in some structures.
Most common issue that we have observed with DSSR is that it places loops in wrong places in some structures. For example, In 2a5p structure, the first loop is identified as reversal by both tools but DSSR also assigns the G6 to this loop which already participates in a tetrad. Such misplacement of tetrad-forming guanines in a loop is also seen in other structures such as 2a5r, 2kpr, 2m53, 2m92, etc (Supplementary Table 2).
The G4 module in DSSR was first developed around 2017-2018 and the work was mentioned briefly in the Lu (2020) paper on DSSR-PyMOL integration. However, due to the funding gap, the development of the G4 module was put on hold. I have never got a chance to write a paper documenting the detailed algorithms for the identification, annotation, and visualization of G-quadruplexes. I recently revamped the G4.x3dna.org website from inside out, and reprocessed all PDB structures to compile the DSSR-G4DB database. Along the way, the G4 module has been updated and improved. Now I'm actively working on a manuscript on the G4 module in DSSR and the associate website.
DSSR has clear definitions of G4-helix and G4-stem, and the corresponding loops. Specifically, for PDB entry 2a5p, DSSR reports the following:
## List of 1 G4-helix
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity,
and may contain more than one G4-stem.
##### Helix#1, 3 G-tetrads, INTRA-molecular, with 1 stem
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
2 glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
3 glyco-bond=-s-- sugar=-3-- groove=wn-- WC-->Major Z- nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19
step#1 pm(>>,forward) area=9.64 rise=3.19 twist=32.7
step#2 pm(>>,forward) area=12.93 rise=3.29 twist=29.4
strand#1 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG4,A.DG5,A.DG6
strand#2 DNA glyco-bond=--s sugar=--3 nts=3 GGG A.DG8,A.DG9,A.DG24
strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG17,A.DG18,A.DG19
Notice the differences in grooves between the first two G-tetrads vs the 3rd one, and the breaking backbone for strand#2 between G9 and G24.
## List of 1 G4-stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity.
Bulges are also allowed along each of the four strands.
##### Stem#1, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
2 glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
step#1 pm(>>,forward) area=9.64 rise=3.19 twist=32.7
strand#1 U DNA glyco-bond=-- sugar=-. nts=2 GG A.DG4,A.DG5
strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9
strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG13,A.DG14
strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG17,A.DG18
loop#1 type=propeller strands=[#1,#2] nts=2 GT A.DG6,A.DT7
loop#2 type=propeller strands=[#2,#3] nts=3 gGA A.DI10,A.DG11,A.DA12
loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG15,A.DT16
Thus the G4-stem consists of two G-tetrads only, and G6 which is part of the 3rd G-tetrad becomes part of a propeller loop. Similar arrangement applies to the other cases.
DSSR also reports the following loop:
## List of 1 non-stem G4-loop (including the two closing Gs)
1 type=diagonal helix=#1 nts=6 GGAAGG A.DG19,A.DG20,A.DA21,A.DA22,A.DG23,A.DG24
In my understanding, the definition and nomenclature of loops in G4 structures are not yet standardized. I am monitoring the development in this field and will update DSSR as needed in due course.
There may also be different types of loops identified by these tools. For example, in 1oz8, which is depicted by CIISGQ as two separate G4s, DSSR fails to identify the G-tetrad, [2, 5, 8, 11], that lies on the outside of the structure. This results in identification of loops formed within this tetrad and its stacking neighbor different to CIIS-GQ. While CIISGQ identifies these loops as reversal, just like the other loops in the structure, DSSR identifies them as non-stem lateral loops. This causes complete misinterpretation of the size and the type of loops in the structure.
The revised DSSR output for PDB entry 1oz8 has the G-tetrad A.DG2,A.DG5,A.DG8,A.DG11 manually added as part of the input, and now all three propeller loops are correctly identified. By default, G11 does not form proper G+G pairs (of LW type cWH or cHW, and Saenger type VI) with G2 and G8. The distortion of the G-tetrad is obvious in the block representation of the structure.
In 4u5m, similar to 1oz8, the structure may be interpreted as two separate G4s connected through a single link (T13,T14). In this case, DSSR identifies only two loops in one of the G4s and labels them as non-stem V-shaped loops. This also differs from CIIS-GQ where CIIS-GQ interprets all loops in both G4 as reversal. Structures containing multiple G4s, such as 1oz8, 4u5m and 6kvb, are often identified with different loop types by DSSR, while CIIS-GQ can recognise the loops correctly and simplifies the comprehension of the structure.
For PDB entry 4u5m, the same arguments above regarding the G4-stem and loops for 2a5p apply.
1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC O+ nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5
2 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6
3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG24,A.DG15,A.DG18,A.DG21
4 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG23,A.DG26,A.DG17,A.DG20
As shown, the backbone between G15 and G26 is broken. Moreover, here the assignment of Gs along the strand may need to be manually adjusted.
As shown in Table 1, by relaxing angle and distance parameters, we were able to identify more tetrads (6T2G, 1OZ8) than DSSR, which detects them as multiplets instead.
The current DSSR results for PDB entry 6t2g and 1oz8 are all as expected. Moreover, DSSR can handle PDB entry 6t2g automatically, while for PDB entry 1oz8 user needs to manually edit the input to include the G-tetrad with G11. By allowing users to specify tetrads, DSSR offers precise control and great flexibility, e.g., to include the G-C-G-C tetrads in PDB entry 1a6h.
DSSR has a detailed explanation of strands, tetrads and loops. However, the comprehensive output of DSSR is often hard to understand and grasp the details of the structure. [in supplemental materials]
The detailed explanations are provided to help users understand the DSSR output. They are most insightful in combination with the schematic block diagrams. For examples, for PDB entry 1a6h, the middle G-C-G-C tetrads are crystal clear with the long green and yellow rectangular blocks, specially along with the detailed annotations of the tetrads, as shown below.
1 glyco-bond=s-s- sugar=---. groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG11,B.DG8,B.DG4
2 glyco-bond=---- sugar=-.-- groove=---- -- -- nts=4 CGCG A.DC2,A.DG10,B.DC9,B.DG3
3 glyco-bond=---- sugar=--.- groove=---- -- -- nts=4 GCGC A.DG3,A.DC9,B.DG10,B.DC2
4 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major -- nts=4 GGGG A.DG4,A.DG8,B.DG11,B.DG1
Another advantage of CIIS-GQ is that it requires only two thresholds, the thresholds of distance and angle parameters that can be modified to detect loosely connected tetrads. Due to this advantage, the identification of the tetrads were possible in at least two structures. In case of 1OZ8, DSSR found three tetrads (G1-G4-G7-G10, G13-G16-G19-G22 and G14-G17-G20-G23) as shown at the result page2 (47) while CIIS-GQ has found one more tetrad which is G2-G5-G8-G11. In comparison DSSR highlighted G5-G8-G11 as a multiplet, omitting the G2. Based on this difference, loop classification differs with CIIS-GQ. DSSR has identified 3 stem reversal loops and 3 non-stem lateral loops while we have identified 7 reversal loops. Stem loop is defined as any loop that also forms a duplex within itself.
DSSR now has PDB entry 1oz8 properly characterized, by manually adding the G-tetrad involving G11, as detailed above.
A similar difference exists in 6T2G. DSSR could find 2 tetrads in this structure (G2-G6-G11-G26 and G4-G9-G13-G28) as shown at the result page3 (47) while CIIS-GQ found one more tetrad, G3-G7-G12-G27. DSSR is able to show these four guanines as a multiplet in the list of multiplets section, however does not present it as a tetrad like the other two tetrads. As a result, CIIS-GQ loop types and placements are also different. DSSR has found six lateral loops while CIIS-GQ has found three reversal loops.
DSSR can now handle PDB entry 6t2g automatically. Previous versions of DSSR missed the G-tetrad (G3+G7+G12+G27) because of the G12+G27 pair: it fails the criteria to be classified as the pair of LW type cWH or cHW and Saenger type VI. Thus G3+G7+G12+G27 do not qualify as a G-tetrad, but they still form a multiplet with four guanines.
References
Direk, T., & Doluca, O. (2024). Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ). Journal of Computer-Aided Molecular Design, 38(1), 35. https://doi.org/10.1007/s10822-024-00573-1
Lu, X.-J. (2020). DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. Nucleic Acids Research, gkaa426. https://doi.org/10.1093/nar/gkaa426
The legacy PDB format has a field called “altLoc” (alternate location indicator) for "ATOM/HETATM" records in the "Coordinate Section". The corresponding documentation is excerpted below:
COLUMNS DATA TYPE FIELD DEFINITION
-----------------------------------------------------------------------
17 Character altLoc Alternate location indicator.
-
AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples).
- For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:
- In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together.
In mmCIF format, AltLoc is under the atom_site category, with attribute name label_alt_id: i.e., labelled as _atom_site.label_alt_id. It is a required data item and appears in 43% of entries in the PDB.
In 3DNA and DSSR, AltLoc has a default value of "A1 ": an atom is taken into consideration if its AltLoc field (a single character) is space, A, or 1, otherwise it is ignored. Note that for mmCIF format, AltLoc field with dot (.) or question mark (?) is taken as space. Customized AltLoc values can be set via the --altloc option in DSSR.
Here is an example. PDB entry 7o1h is a 31-mer synthetic construct, with a hybrid-2R quadruplex-duplex of 3(-P-P-Lw) topology and three syn guanosines. It contains two modified residues designated BGM (BGM26 and BGM28), 8-bromo-2'-deoxyguanosine-5'-monophosphate, with AltLoc set to B. By default, DSSR detects only one G-tetrad, consisting of DG5,DG9,DG13,DG27, ignoring the two G-tetrads with BGM26 and BGM28. With the --altloc=B option (space is always included), all three G-tetrads are detected and the G-quadruplex (a G4-stem) is then automatically annotated as 3(-P-P-Lw):
# x3dna-dssr -i=7o1h-assembly1.cif --altloc=B
List of 2 types of 3 modified nucleotides
nt count list
1 BGM-g 2 A.BGM26,A.BGM28
2 THM-t 1 A.THM1
List of 1 G4-stem
Note: a G4-stem is defined as a G4-helix with backbone connectivity.
Bulges are also allowed along each of the four strands.
stem#1[#1] layers=3 INTRA-molecular loops=3 descriptor=3(-P-P-Lw) note=hybrid-2R(3+1) UUUD hybrid-(mixed)
1 glyco-bond=---s sugar=---. groove=--wn WC-->Major nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28
2 glyco-bond=---s sugar=--.- groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27
3 glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26
step#1 pm(>>,forward) area=13.57 rise=3.39 twist=26.7
step#2 pm(>>,forward) area=12.00 rise=3.44 twist=28.4
strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
strand#3 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG12,A.DG13,A.DG14
strand#4 D DNA glyco-bond=sss sugar=.-- nts=3 gGg A.BGM28,A.DG27,A.BGM26
loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT11
loop#3 type=lateral strands=[#3,#4] nts=11 ACGCGCAGCGT A.DA15,A.DC16,A.DG17,A.DC18,A.DG19,A.DC20,A.DA21,A.DG22,A.DC23,A.DG24,A.DT25
See G4.x3dna.org for DSSR-enabled annotation and visualization of this G4 structure. Here is the G4-stem in the frame of reference of 5' DG4 (bottom right), following the convention of Dvorkin et al. (2018). It is orientated automatically based on the standard base-reference frame (Olson et al. (2001)) of DG4.
References:
- Dvorkin, Scarlett A., Andreas I. Karsisiotis, and Mateus Webba Da Silva. 2018. “Encoding Canonical DNA Quadruplex Structure.” Science Advances 4 (8): eaat3007. https://doi.org/10.1126/sciadv.aat3007.
- Olson, Wilma K, Manju Bansal, Stephen K Burley, Richard E Dickerson, Mark Gerstein, Stephen C Harvey, Udo Heinemann, et al. 2001. “A Standard Reference Frame for the Description of Nucleic Acid Base-Pair Geometry.” Journal of Molecular Biology 313 (1): 229–37. https://doi.org/10.1006/jmbi.2001.4987.
DNA and RNA are biological macromolecules consisting of long chains of nucleotides. In PDB coordinate files, each DNA/RNA chain is assigned a unique identifier. For the legacy PDB format, the size of the chain identifier is clearly defined to be one alphanumeric character. For the mmCIF format, the length of the chain identifier is flexible: it is normally up to 4-char long, but assembly files can have chain identifiers longer than 4 characters (as of May 2022, see examples).
Recently, I was approached with the following bug report where DSSR v2.4-2021nov11 was used:
Processing file '8feo-assembly1.cif'
[i] '8feo-assembly1.cif' taken as in .cif format by file extension.
*** buffer overflow detected ***: terminated
Aborted
I ran a newer version of DSSR (including the current release v2.5.2-2025apr03) on 8feo-assembly1.cif without any issue, as shown below:
# x3dna-dssr -i=8feo-assembly1.cif -o=8feo.out
[i] '8feo-assembly1.cif' taken as in .cif format by file extension.
Processing file '8feo-assembly1.cif'
[w] chain id 'AAA-2' > 4 chars
...
# Excerpt from 8feo.out
no. of DNA/RNA chains: 2 [AAA=16,AAA-2=16]
no. of nucleotides: 32
...
List of 16 base pairs
nt1 nt2 bp name Saenger LW DSSR
1 AAA.A1 AAA-2.U16 A-U WC 20-XX cWW cW-W
2 AAA.G2 AAA-2.C15 G-C WC 19-XIX cWW cW-W
3 AAA.A3 AAA-2.U14 A-U WC 20-XX cWW cW-W
The message [w] chain id 'AAA-2' > 4 chars is saying that the chain identifier ‘AAA-2’ is out of the 4-char limit.
In addition to 8feo, similar issues were also fixed for related PDB entries 5a79, 6a7a, 8feo, 8fep, 8feq, 7umk, and 4v3p. Note that 4v3p is a eukaryotic polyribosomal assembly which takes several hours to run on a MacBookPro with 32GB RAM.
Some background information on how DSSR handles chain identifiers for mmCIF format files
When mmCIF support was first added to DSSR in 2013, I hard-coded the chain identifier to 4 chars following the documentation. In early 2024, when running DSSR on weekly updated PDB entries, I noticed a core dump bug with PDB entry 8feo for its biological assembly 1. At that time, I was not aware of the update on mmCIF-Formatted Assembly Files and its expansion of chain identifiers for symmetry-related copies: with PDB assembly files, -# is appended to any chain that is generated by a symmetry operation. So if the base chain id has 3 chars (e.g., AAA), the symmetry related chain will have 5 chars (e.g., AAA-2).
That is the case for PDB entry 8feo: it has a chain with identifier AAA-2 which is symmetry-related to the asymmetric unit chain AAA. Since AAA-2 (5-char long) is above the hard-coded 4-char limit, DSSR crashed (out of array boundary in C). After recognizing the issue, I've increased the chain identifier limit in DSSR to 8 chars, more than enough for all current PDB entries. Moreover, DSSR performs sanity check of chain identifier length: it reports diagnostic message as shown above for chains with over 4-char identifiers (e.g., AAA-2), and automatically shortens long chains to the enlarged limit. DSSR is now more robust and user friendly: it no longer simply crashes, but communicates helpful info about unusual cases to draw users' attention.
Taking this opportunity, I have also proactively updated DSSR to support long atom names , residue names, and segment ids, in preparation for future id changes. Tracing issues to their root causes and fixing them systematically is a key part that makes DSSR a reliable tool for structural bioinformatics. Tests have been added to the quality control infrastructure to ensure that all these new features work as expected.
Nowadays, the vast majority (over 90%) of users’ questions about DSSR can be answered straight away simply because they have already been addressed in advance, as shown in the above example for long chain identifiers. I'm always on the lookout for issues reported on the 3DNA Forum, received from email, Zoom, or in person, and more systematically via DSSR update on weekly released PDB entries, and uploaded files on the web-services (g4.x3dna.org and skmatic.x3dna.org). Every issue is an opportunity to further polish DSSR and make it better. Overall, users’ feedback is invaluable to me: I take it as an asset instead of a burden.
Documentation on chain identifiers in PDB and mmCIF formats
PDB format
The Coordinate Section in the PDB format documentation contains the following for ATOM/HETATM records:
The ATOM records present the atomic coordinates for standard amino acids and nucleotides. ... Non-polymer chemical coordinates use the HETATM record type.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
-----------------------------------------------------------
22 Character chainID Chain identifier.
**Details**
- Non-blank alphanumerical character is used for chain identifier.
So the chain identifier in PDB format is a single alphanumeric character in column 22 of the ATOM/HETATM records.
mmCIF format
-
Large Structures Represented in mmCIF/PDBx:
Chain identifiers of up to 4 characters are permitted. The PDB chain identifier corresponds to the "_atom_site.auth_asym_id" data item.
-
News item on Distributing PDBx/mmCIF-Formatted Assembly Files
- Github repo on Sample assembly files in PDBx/mmCIF Format
These updated PDBx/mmCIF format assembly files files will include all symmetry generated copies of each chain within a single model, with distinct chain IDs assigned to each. Generation of distinct chain IDs in assembly files are based upon the following rules:
- Chain IDs of the original chains from the atomic coordinate file will be retained (e.g., A)
- Assign unique chain ID for each symmetry copy within a single model. Rules of chain ID assignments:
- The applied index of the symmetry operator will be appended to the original chain ID separated by a dash (e.g., A-2, A-3, etc.)
- If there are more than one type of symmetry operators applied to generate symmetry copy, a dash sign will be used between two operators (e.g., A-12-60, A-60-88, etc.)
Recently, I came across the paper by Mitra et al. (2025) titled "RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions." I am glad to notice that DSSR (Lu et al. 2015) has been cited extensively in this work, as follows:
As part of the processing pipeline, multiple software is run including DSSR^12^ (base-pairing geometries, protein–RNA hydrogen bonds, and RNA secondary structure), HBPLUS^17^ (hydrogen bonds involving water molecules), ... Leontis-Westhof^27^ base pair annotations (as computed by DSSR^12^) ... The structural elements (stems, loops, hairpins, junctions, etc.) are detected using DSSR^12^ and mapped to the partial projection layout (via averaging corresponding residue coordinates)... We explored the relative abundance of different standard nucleotides (A, C, G, and U) in helical vs. non-helical regions (as computed by DSSR^12^)...We quantified the propensity of base-pairing (as detected by DSSR^12^) between different RNA bases (Fig. 3D).
This is an impressive contribution on the characterization of protein-RNA interactions. Reading carefully through the paper and its supplemental PDF, I was intrigued by the following note on a water-mediated U-U base pair missed by DSSR.
Another important aspect to discuss is RNA–RNA water-mediated interactions^33,34^. ... One such example is the CUG repeat structure from PDB ID 7Y2B^35^ (Fig. S5A). The U/U mismatches in this structure are often unable to form direct hydrogen bonds (specifically, the central U/U mismatch forms no direct hydrogen bond). Therefore, DSSR^12^ does not classify it as a base pair. However, two water molecules form water-mediated hydrogen bonds between the two U bases. ...
While DSSR internally already takes consideration of water-mediated H-bonds in the detection of base pairs, it still requires: (1) at least one direct H-bond between two base atoms or a base atom to backbone, and (2) a co-planar geometry between the two bases. The water-mediated U7-U7 pair in PDB entry 7Y2B does not fulfill condition (1): the minimal distance between the two U bases is 5 Å, which is far larger than a typical H-bonding distance. Therefore, DSSR did not classify it as a base pair.
Prompted by the observation of Mitra et al. (2025), I have added a new option (--pair-water) in the DSSR v2.5.1-2025mar19 release to allow for water-mediated base pairs to be detected. Using PDB entry 7Y2B as an example, the DSSR command and related base-pairs output are shown below.
# x3dna-dssr -i=7Y2B.pdb1 --symm --pair-water
List of 13 base pairs
nt1 nt2 bp name Saenger LW DSSR
1 1:S.U1 2:S.A13 U-A WC 20-XX cWW cW-W
2 1:S.U2 2:S.A12 U-A WC 20-XX cWW cW-W
3 1:S.C3 2:S.G11 C-G WC 19-XIX cWW cW-W
4 1:S.U4 2:S.U10 U-U -- -- cWW cW-W
5 1:S.G5 2:S.C9 G-C WC 19-XIX cWW cW-W
6 1:S.C6 2:S.G8 C-G WC 19-XIX cWW cW-W
7 1:S.U7 2:S.U7 U-U Water -- cWW cW-W
8 1:S.G8 2:S.C6 G-C WC 19-XIX cWW cW-W
9 1:S.C9 2:S.G5 C-G WC 19-XIX cWW cW-W
10 1:S.U10 2:S.U4 U-U -- -- cWW cW-W
11 1:S.G11 2:S.C3 G-C WC 19-XIX cWW cW-W
12 1:S.A12 2:S.U2 A-U WC 20-XX cWW cW-W
13 1:S.A13 2:S.U1 A-U WC 20-XX cWW cW-W
Base pair #7 is water-mediated, as shown in the molecular image below. Note that .pdb1 means biological unit 1, and the option --symm reads the two symmetry-related structures in the MODEL/ENDMDL delineated ensemble as a single structure. See the DSSR User Manual for more details.
References
-
Lu, Xiang-Jun, Harmen J. Bussemaker, and Wilma K. Olson. 2015. “DSSR: An Integrated Software Tool for Dissecting the Spatial Structure of RNA.” Nucleic Acids Research, July, gkv716. https://doi.org/10.1093/nar/gkv716.
- Mitra, Raktim, Ari S. Cohen, Wei Yu Tang, Hirad Hosseini, Yongchan Hong, Helen M. Berman, and Remo Rohs. 2025. “RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions.” Journal of Molecular Biology, February, 169012. https://doi.org/10.1016/j.jmb.2025.169012.
Cover images provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
See the 2020 paper titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" in Nucleic Acids Research and the corresponding Supplemental PDF for details. Many thanks to Drs. Wilma Olson and Cathy Lawson for their help in the preparation of the illustrations.
Details on how to reproduce the cover images are available on the 3DNA Forum.
Structure of the human minor spliceosome pre-B complex (PDB id: 8Y7E; Bai R, Yuan M, Zhang P, Luo T, Shi Y, Wan R. 2024. Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science 383: 1245–1252). The protein–RNA assembly reveals the mechanisms of recognition and recruitment of several small nuclear ribonucleoproteins (snRNPs) involved in the splicing of U12-type introns. The pre-mRNA is depicted by a red ribbon, and the U12 small nuclear RNA (snRNA) by a green ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the proteins are shown as gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Human tRNA splicing endonuclease (TSEN) complex bound to pre-tRNAArg (PDB id: 7UXA; Hayne CK, Butay KJ, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE. 2023. Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. Nat Struct Mol Biol 30: 824–833). Cryo-EM structure of the TSEN protein assembly with pre-tRNAArg provides insights into the recognition and splicing of an intron that must be removed from the pre-tRNA before translation. The pre-tRNAArg is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the TSEN subunits are shown as gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Systemic RNA interference defective protein 1 (SID1) in complex with dsRNA (PDB id: 8XC1; Wang R, Cong Y, Qian D, Yan C, Gong D. 2024. Structural basis for double-stranded RNA recognition by SID1. Nucleic Acids Res 52: 6718–6727). The cryo-EM structure provides a major step towards understanding the mechanism of dsRNA recognition by SID1, involving extensive interactions between basic amino-acid residues and the sugar-phosphate backbone. The dsRNA chains are depicted by red, green, blue, and yellow ribbons, with bases and Watson-Crick base pairs represented as color-coded blocks and minor-groove edges colored white: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; SID1 is shown by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Complex of arginyl-tRNA-protein transferase 1 (ATE1) with tRNAArg and a short peptide substrate (PDB id: 8UAU; Lan X, Huang W, Kim SB, Fu D, Abeywansha T, Lou J, Balamurugan U, Kwon YT, Ji CH, Taylor DJ, Zhang Y. 2024. Oligomerization and a distinct tRNA-binding loop are important regulators of human arginyl-transferase function. Nat Commun 15: 6350). The ATE1 homodimer dissociates upon binding the peptide and forms a loop that wraps around tRNAArg. The tRNAArg is depicted by a red ribbon, with bases and Watson–Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; ATE1 is shown by a gold ribbon and the peptide by a white ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Structure of endoribonuclease P (RNase P) in complex with pre-tRNAHis-Ser (PDB id: 8CBK; Meynier V, Hardwick SW, Catala M, Roske JJ, Oerum S, Chirgadze DY, Barraud P, Yue WW, Luisi BF, Tisné C. 2024. Structural basis for human mitochondrial tRNA maturation. Nat Commun 15: 4683). The structure reveals the first step of human mitochondrial tRNA maturation by RNase P, processing the 5′-leader of pre-tRNA. The RNA is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the protein assembly is shown by the gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Structure of a group II intron ribonucleoprotein in the pre-ligation state (PDB id: 8T2R; Xu L, Liu T, Chung K, Pyle AM. 2023. Structural insights into intron catalysis and dynamics during splicing. Nature 624: 682–688). The pre-ligation complex of the Agathobacter rectalis group II intron reverse transcriptase/maturase with intron and 5′-exon RNAs makes it possible to construct a picture of the splicing active site. The intron is depicted by a green ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the 5′-exon is shown by white spheres and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Complex of terminal uridylyltransferase 7 (TUT7) with pre-miRNA and Lin28A (PDB id: 8OPT; Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJ. 2024. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 31: 1426–1438). The RNA-binding pluripotency factor LIN28A invades and melts the RNA and affects the mechanism of action of the TUT7 enzyme. The RNA backbone is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; TUT7 is represented by a gold ribbon and LIN28A by a white ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Cryo-EM structure of the pre-B complex (PDB id: 8QP8; Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SE, Urlaub H, Kastner B, Stark H, Lührmann R. 2024. Structural insights into the cross-exon to cross-intron spliceosome switch. Nature 630: 1012–1019). The pre-B complex is thought to be critical in the regulation of splicing reactions. Its structure suggests how the cross-exon and cross-intron spliceosome assembly pathways converge. The U4, U5, and U6 snRNA backbones are depicted respectively by blue, green, and red ribbons, with bases and Watson-Crick base pairs shown as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the proteins are represented by gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Structure of the Hendra henipavirus (HeV) nucleoprotein (N) protein-RNA double-ring assembly (PDB id: 8C4H; Passchier TC, White JB, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. 2024. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 14: 14099). The HeV N protein adopts a bi-lobed fold, where the N- and C-terminal globular domains are bisected by an RNA binding cleft. Neighboring N proteins assemble laterally and completely encapsidate the viral genomic and antigenomic RNAs. The two RNAs are depicted by green and red ribbons. The U bases of the poly(U) model are shown as cyan blocks. Proteins are represented as semitransparent gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Structure of the helicase and C-terminal domains of Dicer-related helicase-1 (DRH-1) bound to dsRNA (PDB id: 8T5S; Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. 2024. Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. eLife 13: RP93979. Cryo-EM structures of Dicer-1 in complex with DRH-1, RNAi deficient-4 (RDE-4), and dsRNA provide mechanistic insights into how these three proteins cooperate in antiviral defense. The dsRNA backbone is depicted by green and red ribbons. The U-A pairs of the poly(A)·poly(U) model are shown as long rectangular cyan blocks, with minor-groove edges colored white. The ADP ligand is represented by a red block and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
Moreover, the following 30 [12(2021) + 12(2022) + 6(2023)] cover images of the RNA Journal were generated by the NAKB (nakb.org).
Cover image provided by the Nucleic Acid Database (NDB)/Nucleic Acid Knowledgebase (NAKB; nakb.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).
DSSR produces RNA secondary structures in connect table (.ct) format. According to "RNAstructure Command Line Help: File Formats" (with slight editing):
CT File Format
A CT (Connectivity Table) file contains secondary structure information for a sequence. These files are saved with a CT extension. When entering a structure to calculate the free energy, the following format must be followed.
- Start of first line: number of bases in the sequence
- End of first line: title of the structure
- Each of the following lines provides information about a given base in the sequence. Each base has its own line, with these elements in order:
- Base number: index n
- Base (A, C, G, T, U, X)
- Index n-1
- Index n+1
- Number of the base to which n is paired. No pairing is indicated by 0 (zero).
- Natural numbering. RNAstructure ignores the actual value given in natural numbering, so it is easiest to repeat n here.
Using PDB entry 1msy as an example (see Figure 1 below):
Figure 1. 3D and 2D structures of PDB entry 1msy. (A) 3D schematic auto-created via the DSSR-PyMOL integration. The labeled residues follow PDB coordinates. (B) 2D diagram rendered with VARNA using DSSR-derived 2D structural information in the .ct format. This figure was annotated using Inkscape.
With commands:
x3dna-dssr -i=1msy.pdb
cp dssr-2ndstrs.ct 1msy-dssr-default.ct
The file 1msy-dssr-default.ct has the following contents:
27 ENERGY = 0.0 [1msy] -- secondary structure derived by DSSR
1 U 0 2 0 2647
2 G 1 3 26 2648
3 C 2 4 25 2649
4 U 3 5 24 2650
5 C 4 6 23 2651
6 C 5 7 22 2652
7 U 6 8 0 2653
8 A 7 9 0 2654
9 G 8 10 0 2655
10 U 9 11 0 2656
11 A 10 12 0 2657
12 C 11 13 17 2658
13 G 12 14 0 2659
14 U 13 15 0 2660
15 A 14 16 0 2661
16 A 15 17 0 2662
17 G 16 18 12 2663
18 G 17 19 0 2664
19 A 18 20 0 2665
20 C 19 21 0 2666
21 C 20 22 0 2667
22 G 21 23 6 2668
23 G 22 24 5 2669
24 A 23 25 4 2670
25 G 24 26 3 2671
26 U 25 27 2 2672
27 G 26 0 0 2673
Here the first line contains 27 (as the number of bases) and ENERGY = 0.0 [1msy] -- secondary structure derived by DSSR (as the title). While RNAstructure ignores the actual values given in natural numbering, DSSR outputs the residue numbers of the nucleotides (e.g. U2467 and G2673) in the PDB file.
With the DSSR option --structure-title (or --str-title, actually via regex "^-?-?str(ucture)?[-_]?title"), users can set the title for the derived .ct file, as shown below:
x3dna-dssr -I=1msy.pdb --structure-title='CT file derived from DSSR'
cp dssr-2ndstrs.ct 1msy-dssr-title.ct
27 CT file derived from DSSR
1 U 0 2 0 2647
2 G 1 3 26 2648
......
26 U 25 27 2 2672
27 G 26 0 0 2673
One can also remove the title, by using an empty string "" (i.e., --str-title="") or simply --str-title (or --str-title=).
x3dna-dssr -I=1msy.pdb --structure-title=""
cp dssr-2ndstrs.ct 1msy-dssr-notitle.ct
27
1 U 0 2 0 2647
2 G 1 3 26 2648
......
With the --more option, DSSR also outputs additional info that can be used to easily identify a nucleotide and its pairing partner.
x3dna-dssr -I=1msy.pdb --more --structure-title="1msy with extra info"
cp dssr-2ndstrs.ct 1msy-dssr-extra.ct
27 1msy with extra info
1 U 0 2 0 2647 # name=A.U2647
2 G 1 3 26 2648 # name=A.G2648, pairedNt=A.U2672
3 C 2 4 25 2649 # name=A.C2649, pairedNt=A.G2671
......
Note that unlike for the .bpseq format with extra info which cannot be fed directly into VARNA, the extra info for the .ct format causes no troubles for VARNA to visualize the 2d structure.
The --structure-title option is another small feature implemented in DSSR. It is currently not documented in the DSSR User Manual since this feature is unlikely of general interest.
DSSR commands used, and the output .ct files:
x3dna-dssr -i=1msy.pdb
cp dssr-2ndstrs.ct 1msy-dssr-default.ct
x3dna-dssr -I=1msy.pdb --structure-title='CT file derived from DSSR'
cp dssr-2ndstrs.ct 1msy-dssr-title.ct
x3dna-dssr -I=1msy.pdb --structure-title=""
cp dssr-2ndstrs.ct 1msy-dssr-notitle.ct
x3dna-dssr -I=1msy.pdb --more --structure-title="1msy with extra info"
cp dssr-2ndstrs.ct 1msy-dssr-extra.ct
By default, DSSR produces RNA secondary structures in three commonly used file formats––ViennaRNA package dbn, Mfold connect table (.ct), and CRW bpseq––that can be fed directly into visualization tools such as VARNA. In this blog post, I want to dig deeper into the bpseq format, and show the variations available from DSSR.
According to "RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database" (with slight editing):
BPSEQ format:The file name should end with the suffix ".bpseq", as in "mystr.bpseq". The bpseq format is a simple text format in which there is one line per base in the molecule, listing the position of the base (leftmost position is 1), the base name (A,C,G,U, or other alphabetical characters), and the position number of the base to which it is paired, with a 0 denoting that the base is unpaired. For more information, see the Comparative RNA Web Site. An example is as follows:
1 G 8
2 G 7
3 C 0
4 A 0
5 U 0
6 U 0
7 C 2
8 C 1
For complexes with more than one molecule, the molecules are listed in sequence, with the base pairs numbers of each successive molecule following in order from the previous molecule.
The bases in bpseq format are identified by position numbers starting from 1 for the leftmost position. That is the convention DSSR follows by default in its .bpseq output. For example, for the PDB entry 1msy, which contains 27 nucleotides, the command x3dna-dssr -i=1msy.pdb will generate a file named dssr-2ndstrs.bpseq with the following contents (abbreviated):
1 U 0
2 G 26
3 C 25
......
25 G 3
26 U 2
27 G 0
However, according to PDB atomic coordinates, the nucleotides are numbered from U2647 (#1) to G2673 (#27) as shown in the Figure 1 below:
Figure 1. 3D and 2D structures of PDB entry 1msy. (A) 3D schematic auto-created via the DSSR-PyMOL integration. The labeled residues follow PDB coordinates. (B) 2D diagram rendered with VARNA using DSSR-derived 2D structural information in the .ct format. This figure was annotated using Inkscape.
It makes sense that the labelling of bases in the 2D bpseq format follows those from the 3D atomic coordinates in the PDB. Thus instead of starting from position 1 as shown above, the bpseq file would start with 2647. That's exactly what the DSSR --bpseq option is created for. Thus, with the command x3dna-dssr -i=1msy.pdb --bpseq, the output file dssr-2ndstrs.bpseq now has the following contents (abbreviated):
2647 U 0
2648 G 2672
2649 C 2671
......
2671 G 2649
2672 U 2648
2673 G 0
This .bpseq file can be read by VARNA (tested with VARNAv3-93.jar) to generate a 2D image as shown in Figure 1(B) above.
Moreover, with the command x3dna-dssr -i=1msy.pdb --bpseq=extra, the output file dssr-2ndstrs.bpseq now contains additional info to easily identify a nucleotide and its pairing partner:
2647 U 0 # name=A.U2647
2648 G 2672 # name=A.G2648, pairedNt=A.U2672
2649 C 2671 # name=A.C2649, pairedNt=A.G2671
......
2671 G 2649 # name=A.G2671, pairedNt=A.C2649
2672 U 2648 # name=A.U2672, pairedNt=A.G2648
2673 G 0 # name=A.G2673
It should be noted that this .bpseq output file is no longer compliant to the standard, and can not be fed into VARNA for visualization.
The --bpseq option has been added upon users' request. The --bpseq=extra variation was implemented recently to ensure that the --bpseq option by itself produce a valid .bpseq file without extra info (e.g., enabled with the global --more option). Now the extra info for .bpseq output is enabled only by setting --bpseq=extra explicitly.
This --bpseq option and its evolution is a good example of how DSSR responds to community requests. I'm here to listen and I'm always willing to improve DSSR that better fit users' needs. If you make use of DSSR in your pipeline and need some adaptions, please do not hesitate to contact me. I may consider adding a new option or revising the code otherwise that would streamline the integration of DSSR into your project.
DSSR commands used, and the output .bpseq files:
x3dna-dssr -i=1msy.pdb
cp dssr-2ndstrs.bpseq 1msy-dssr-default.bpseq
x3dna-dssr -i=1msy.pdb --bpseq
cp dssr-2ndstrs.bpseq 1msy-dssr-bpseq.bpseq
x3dna-dssr -i=1msy.pdb --bpseq=extra
cp dssr-2ndstrs.bpseq 1msy-dssr-bpseq-extra.bpseq
By following citations to 3DNA/DSSR, I recently came across the paper "RNAtango: Analysing and comparing RNA 3D structures via torsional angles" in PLOS Computational Biology by Mackowiak M, Adamczyk B, Szachniuk M, and Zok T. This work provides a nice summary of definitions of torsion and pseudo-torsion angles in RNA structure, and an angular metrics (MCQ, Mean of Circular Quantities) to score structure similarity. The RNAtango web application allows user to explore the distribution of torsion angles in a single structure/fragment (Single model), compare RNA models with a native structure (Models vs Target), or perform a comparative analysis in a set of models (Model vs Model).
In the Introduction section, 3DNA/DSSR are mentioned along with other related tools, as below:
Several bioinformatics tools have been designed for analyzing torsion and pseudotorsion angles, each with its own strengths and limitations. 3DNA, an open-source toolkit, provides comprehensive functionality, including torsion and pseudotorsion angle calculations [27], but lacks support for the current standard PDBx/mmCIF file format. DSSR, the successor to 3DNA, overcomes this limitation by supporting both PDB and PDBx/mmCIF files. However, it is a closed-source, commercial application that requires licensing, even for research purposes [28]. Curves+, another tool used for torsion angle analysis, is currently inaccessible due to the unavailability of its webpage and source code hosting [29]. Barnaba, a Python library and toolset for analyzing single structures or trajectories, supports torsion angle calculations but, like 3DNA, does not support the PDBx/mmCIF format [30]. For users seeking a more user friendly option, AMIGOS III offers a PyMOL plugin that calculates pseudotorsion angles and presents them in Ramachandran-like plots [17].
Every bioinformatic software has been developed for a specific purpose, and no two such tools can be identical. It is a good thing that the community has a choice for RNA backbone analysis. Indeed, 3DNA has been superseded by DSSR, which is licensed by Columbia Technology Ventures (CTV) to ensure its continuous development and availability. However, DSSR remain competitive due to its unmatched functionality, usability, and support: it saves users a substantial amount of time and effort when compared to other options.
From the very beginning, it has been my dream to make DSSR stand out for its quality and value, and be widely accessible. The CTV DSSR distribution by no means follow typical commercial license for a software product: specifically, it does not include a license key to limit DSSR's usage to a specific machine and operating system, and there is no expire date for the software either. Moreover, the Basic Academic license was free of charge when DSSR was initially licensed by the CTV in August 2020, and remained so until around end of 2021 when the web-based "Express Licenses" functionality no longer worked. Manually handling the large number of requests for free academic licenses was not sustainable, and that was when the DSSR Basic Academic free license was removed. Upon user requests, we late on re-introduced DSSR Basic Academic license, but with a one-time fee of $200 to cover the running cost. That may be reason for the remark in the RNAtango paper that DSSR "requires licensing, even for research purposes".
With the recent NIH R24 funding support on "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids", we are providing DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing". Checking the list of licensees, I am thrilled to see the many new DSSR users from leading institutions around the world, including Stockholm University, Ghent University, Universitaet Heidelberg, University of Palermo, CSSB-Hamburg, Nicolaus Copernicus University, NIH, Harvard, ... Clearly, DSSR fills a niche, and the demands for it remain strong!
Back to torsion angles, it is safe to say that DSSR has unique features not available or easily accessible elsewhere. Here are some use cases using tRNA PDB entry 1ehz as an example:
x3dna-dssr -i=1ehz.cif # generate dssr-torsions.txt among other output files
x3dna-dssr -i=1ehz.cif --torsion-file -o=1ehz-torsions.txt # just the torsion file 1ehz-torsions.txt
x3dna-dssr -i=1ehz.cif --json | jq .nts[54] > 1ehz-PSU55.txt # DSSR-derived features for nucleotide PSU55
Users can easily run the DSSR commands listed above and get the results in human-readable text and machine-friendly JSON formats. For verification, the contents of 1ehz-torsions.txt and 1ehz-PSU55.txt are available by clicking the links.
It is worth noting that DSSR has the --nmr option for the analysis of an ensemble of NMR structures, in .pdb or .cif format, as deposited in the PDB. The combination of --nmr and --json renders DSSR easily accessible to the molecular dynamics (MD) community.
In principle, calculating torsion angles is a straightforward process. In reality, factors such as modified nucleotides (especially pseudouridine), missing atoms, NMR ensembles or MD trajectories, PDB vs mmCIF formats, etc. make the implementation complicated. Without paying great attention to details, it is easy to make subtle mistakes. For example, with RNAtango the chi (χ) torsion angle for A.PSU55 of 1ehz is listed as -152.42°, which is wrong. The correct value should be -147.0° as reported by DSSR (see below and the link 1ehz-PSU55.txt above).
DSSR provides a comprehensive list of backbone parameters (as listed below for 1ehz). The program is efficient and robust, and has been battle tested. I am always quick to fix any bugs once verified, and am willing to add new features once thoroughly studied. In short, DSSR has been designed to be a reliable tool that the community can trust and build upon.
DSSR-derived backbone features for tRNA 1ehz:
Output of DNA/RNA backbone conformational parameters
DSSR v2.4.5-2024sep24 by xiangjun@x3dna.org
******************************************************************************************
Main chain conformational parameters:
alpha: O3'(i-1)-P-O5'-C5'
beta: P-O5'-C5'-C4'
gamma: O5'-C5'-C4'-C3'
delta: C5'-C4'-C3'-O3'
epsilon: C4'-C3'-O3'-P(i+1)
zeta: C3'-O3'-P(i+1)-O5'(i+1)
e-z: epsilon-zeta (BI/BII backbone classification)
chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4
Range [170, -50(310)] is assigned to anti, and [50, 90] to syn
phase-angle: the phase angle of pseudorotation and puckering
sugar-type: ~C2'-endo for C2'-endo like conformation, or
~C3'-endo for C3'-endo like conformation
Note the ONE column offset (for easy visual distinction)
ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom
(P) expressed in the standard reference frame of the 5' base; the value is
POSITIVE when P lies on the +z-axis side (base in anti conformation);
NEGATIVE if P is on the -z-axis side (base in syn conformation)
Dp: perpendicular distance of the 3' P atom to the glycosidic bond
[Ref: Chen et al. (2010): "MolProbity: all-atom structure
validation for macromolecular crystallography."
Acta Crystallogr D Biol Crystallogr, 66(1):12-21]
splay: angle between the bridging P to the two base-origins of a dinucleotide.
nt alpha beta gamma delta epsilon zeta e-z chi phase-angle sugar-type ssZp Dp splay
1 G A.G1 --- -128.1 67.8 82.9 -155.6 -68.6 -87(BI) -167.8(anti) 16.1(C3'-endo) ~C3'-endo 4.59 4.57 24.92
2 C A.C2 -67.4 -178.4 53.8 83.4 -145.1 -76.8 -68(BI) -163.8(anti) 16.1(C3'-endo) ~C3'-endo 4.52 4.63 21.15
3 G A.G3 -74.5 169.7 59.5 80.7 -148.3 -80.0 -68(BI) -161.9(anti) 14.6(C3'-endo) ~C3'-endo 4.75 4.69 22.28
4 G A.G4 -64.4 162.2 60.7 82.2 -157.4 -68.7 -89(BI) -168.7(anti) 20.8(C3'-endo) ~C3'-endo 4.68 4.57 25.22
5 A A.A5 -74.7 -176.5 53.4 84.9 -137.5 -81.7 -56(BI) -162.9(anti) 4.8(C3'-endo) ~C3'-endo 4.49 4.76 22.04
6 U A.U6 -48.8 157.6 55.3 81.3 -151.0 -77.0 -74(BI) -160.0(anti) 18.2(C3'-endo) ~C3'-endo 4.31 4.51 22.89
7 U A.U7 -59.5 -178.7 62.5 137.3 -105.9 -52.0 -54(--) -133.1(anti) 156.1(C2'-endo) ~C2'-endo 1.55 1.41 126.99
8 U A.U8 -83.8 -145.6 55.4 78.6 -142.8 -118.6 -24(--) -161.5(anti) 10.5(C3'-endo) ~C3'-endo 4.60 4.76 62.37
9 A A.A9 -69.7 -141.7 52.3 147.8 -106.2 -77.3 -29(--) -70.5(anti) 149.8(C2'-endo) ~C2'-endo 1.00 1.14 57.38
10 g A.2MG10 177.8 147.2 60.1 89.3 -126.2 -88.7 -37(--) 169.6(anti) 6.6(C3'-endo) ~C3'-endo 4.68 4.63 23.87
11 C A.C11 -56.1 167.9 48.2 87.2 -150.5 -69.9 -81(BI) -160.9(anti) 16.8(C3'-endo) ~C3'-endo 4.28 4.46 21.20
12 U A.U12 -67.8 172.9 51.8 80.7 -158.5 -65.2 -93(BI) -158.3(anti) 25.2(C3'-endo) ~C3'-endo 4.29 4.45 21.01
13 C A.C13 166.6 -169.9 178.6 82.5 -153.1 -97.4 -56(BI) -168.3(anti) 23.7(C3'-endo) ~C3'-endo 4.28 4.36 31.59
14 A A.A14 83.4 -158.3 -114.6 92.0 -125.5 -57.3 -68(--) -170.7(anti) 358.9(C2'-exo) ~C3'-endo 4.67 4.74 38.01
15 G A.G15 -55.1 162.5 51.9 79.8 -136.3 -143.9 8(--) -164.5(anti) 16.0(C3'-endo) ~C3'-endo 4.72 4.74 26.17
16 u A.H2U16 -6.1 91.2 76.8 96.8 -61.8 -131.2 69(--) -85.8(anti) 18.8(C3'-endo) ~C3'-endo -0.71 3.38 145.77
17 u A.H2U17 27.8 107.7 174.1 94.8 178.0 76.2 102(--) -142.5(anti) 341.4(C2'-exo) ~C3'-endo -0.90 4.20 105.55
18 G A.G18 45.4 -159.4 59.0 150.6 -95.2 -179.1 84(BII) -99.5(anti) 154.3(C2'-endo) ~C2'-endo 1.60 1.09 51.64
19 G A.G19 -71.4 -178.9 53.8 153.8 -91.6 -83.7 -8(--) -80.3(anti) 167.6(C2'-endo) ~C2'-endo -1.14 0.48 130.30
20 G A.G20 -81.3 -150.7 47.8 89.9 -122.3 -54.1 -68(--) 177.8(anti) 8.7(C3'-endo) ~C3'-endo 4.90 4.76 57.04
21 A A.A21 -75.6 148.6 -176.6 78.2 -168.9 -75.6 -93(BI) -160.2(anti) 13.0(C3'-endo) ~C3'-endo 4.00 4.26 40.66
22 G A.G22 158.8 153.5 179.3 82.0 -145.0 -80.4 -65(BI) -175.5(anti) 353.8(C2'-exo) ~C3'-endo 4.60 4.73 25.62
23 A A.A23 -53.3 174.8 52.5 82.3 -155.3 -66.4 -89(BI) -158.0(anti) 12.6(C3'-endo) ~C3'-endo 4.18 4.61 22.96
24 G A.G24 -68.8 178.2 46.8 83.6 -144.3 -72.8 -71(BI) -160.7(anti) 13.4(C3'-endo) ~C3'-endo 4.63 4.74 20.51
25 C A.C25 -65.1 168.9 53.9 83.3 -145.1 -68.4 -77(BI) -160.3(anti) 17.4(C3'-endo) ~C3'-endo 4.56 4.70 30.70
26 g A.M2G26 -53.8 170.8 47.7 86.0 -136.3 -76.9 -59(BI) -163.4(anti) 9.3(C3'-endo) ~C3'-endo 4.57 4.67 27.36
27 C A.C27 -53.0 166.9 43.6 83.4 -148.5 -73.4 -75(BI) -168.2(anti) 18.3(C3'-endo) ~C3'-endo 4.53 4.62 23.07
28 C A.C28 -72.4 178.3 49.3 80.1 -152.1 -67.0 -85(BI) -160.6(anti) 9.2(C3'-endo) ~C3'-endo 4.55 4.73 21.61
29 A A.A29 -66.6 174.0 55.6 81.4 -155.5 -78.3 -77(BI) -165.9(anti) 13.7(C3'-endo) ~C3'-endo 4.73 4.65 26.96
30 G A.G30 -54.0 165.9 56.9 83.6 -144.7 -62.3 -82(BI) -171.7(anti) 14.5(C3'-endo) ~C3'-endo 4.67 4.65 25.72
31 A A.A31 -69.9 177.8 52.3 83.7 -137.0 -75.5 -61(BI) -156.7(anti) 14.6(C3'-endo) ~C3'-endo 4.24 4.72 21.52
32 c A.OMC32 -52.7 161.4 49.3 80.1 -145.9 -71.2 -75(BI) -149.9(anti) 20.4(C3'-endo) ~C3'-endo 4.16 4.63 25.94
33 U A.U33 -67.7 -177.0 47.0 82.1 -148.0 -53.7 -94(BI) -148.2(anti) 13.3(C3'-endo) ~C3'-endo 4.19 4.64 75.47
34 g A.OMG34 171.1 148.1 52.5 83.4 -132.5 -71.8 -61(BI) -171.2(anti) 12.2(C3'-endo) ~C3'-endo 4.15 4.58 22.09
35 A A.A35 -47.7 163.7 40.2 80.9 -143.7 -59.5 -84(BI) -154.4(anti) 21.9(C3'-endo) ~C3'-endo 4.20 4.54 20.57
36 A A.A36 -52.4 165.7 51.3 72.2 -160.4 -85.2 -75(BI) -158.4(anti) 45.8(C4'-exo) ~C3'-endo 4.49 4.31 24.48
37 g A.YYG37 -57.5 163.0 47.8 81.1 -148.1 -67.0 -81(BI) -168.8(anti) 15.4(C3'-endo) ~C3'-endo 4.63 4.65 32.08
38 A A.A38 -61.8 -180.0 46.9 82.5 -136.8 -76.4 -60(BI) -169.4(anti) 2.4(C3'-endo) ~C3'-endo 4.63 4.78 23.75
39 P A.PSU39 -47.7 160.4 53.3 79.3 -140.1 -68.6 -72(BI) -165.6(anti) 15.8(C3'-endo) ~C3'-endo 4.55 4.68 26.68
40 c A.5MC40 -67.4 172.0 56.2 83.2 -154.2 -74.9 -79(BI) -162.6(anti) 17.3(C3'-endo) ~C3'-endo 4.52 4.60 27.71
41 U A.U41 -68.2 -179.4 52.4 78.9 -137.3 -84.7 -53(BI) -169.0(anti) 13.4(C3'-endo) ~C3'-endo 4.54 4.75 24.14
42 G A.G42 -47.9 158.7 55.6 79.8 -160.3 -70.3 -90(BI) -169.0(anti) 20.9(C3'-endo) ~C3'-endo 4.43 4.51 23.54
43 G A.G43 -67.0 -178.3 55.6 81.6 -154.9 -76.4 -78(BI) -160.2(anti) 12.6(C3'-endo) ~C3'-endo 4.24 4.61 20.95
44 A A.A44 -59.7 162.1 60.0 85.3 -142.8 -57.2 -86(BI) -159.4(anti) 16.9(C3'-endo) ~C3'-endo 4.25 4.61 31.07
45 G A.G45 -71.9 -176.9 51.0 87.6 -135.1 -78.7 -56(BI) -149.3(anti) 15.4(C3'-endo) ~C3'-endo 4.01 4.58 40.27
46 g A.7MG46 -56.8 -146.5 48.4 141.6 -102.7 -137.9 35(--) -65.8(anti) 154.5(C2'-endo) ~C2'-endo 0.21 0.96 139.04
47 U A.U47 62.4 -164.0 44.4 146.1 -93.7 -78.0 -16(--) -112.0(anti) 164.9(C2'-endo) ~C2'-endo 0.26 0.39 157.37
48 C A.C48 -73.5 -174.3 161.5 145.6 -143.5 75.6 141(--) -140.1(anti) 158.2(C2'-endo) ~C2'-endo 1.92 1.80 147.54
49 c A.5MC49 50.7 168.5 42.2 84.3 -145.0 -82.1 -63(BI) -173.6(anti) 10.1(C3'-endo) ~C3'-endo 4.77 4.75 25.83
50 U A.U50 -51.7 177.2 42.1 80.4 -150.6 -67.8 -83(BI) -165.3(anti) 5.6(C3'-endo) ~C3'-endo 4.38 4.75 23.15
51 G A.G51 -63.9 176.8 52.8 79.4 -150.4 -71.3 -79(BI) -156.6(anti) 11.5(C3'-endo) ~C3'-endo 4.44 4.67 21.28
52 U A.U52 -64.7 173.6 48.5 80.3 -156.5 -69.4 -87(BI) -164.0(anti) 14.1(C3'-endo) ~C3'-endo 4.64 4.74 25.47
53 G A.G53 -56.9 171.5 56.2 83.9 -159.4 -64.9 -95(BI) -169.2(anti) 19.8(C3'-endo) ~C3'-endo 4.59 4.57 24.53
54 t A.5MU54 -79.7 -172.8 57.7 77.6 -128.6 -70.7 -58(BI) -161.5(anti) 20.6(C3'-endo) ~C3'-endo 4.56 4.80 30.73
55 P A.PSU55 -49.7 168.8 44.1 76.6 -140.8 -69.9 -71(BI) -147.0(anti) 10.1(C3'-endo) ~C3'-endo 4.15 4.74 71.28
56 C A.C56 166.4 171.8 53.3 83.4 -132.7 -70.6 -62(BI) -161.5(anti) 12.6(C3'-endo) ~C3'-endo 4.37 4.76 28.07
57 G A.G57 -65.7 167.1 57.5 81.7 -145.2 -67.6 -78(BI) -159.3(anti) 12.8(C3'-endo) ~C3'-endo 4.36 4.65 42.47
58 a A.1MA58 -60.8 -146.1 71.8 156.7 -78.3 -169.3 91(BII) -86.3(anti) 161.1(C2'-endo) ~C2'-endo 0.48 0.68 73.92
59 U A.U59 72.6 -158.8 63.7 84.6 -148.8 -53.7 -95(BI) -165.6(anti) 25.8(C3'-endo) ~C3'-endo 4.67 4.42 27.88
60 C A.C60 -72.2 179.5 66.0 148.3 -97.1 -66.4 -31(--) -117.8(anti) 154.8(C2'-endo) ~C2'-endo 0.99 0.86 90.64
61 C A.C61 -84.3 179.8 38.2 83.0 -152.3 -74.5 -78(BI) -166.7(anti) 14.8(C3'-endo) ~C3'-endo 4.45 4.52 25.80
62 A A.A62 -60.1 179.6 46.9 80.5 -145.6 -74.1 -71(BI) -158.7(anti) 9.9(C3'-endo) ~C3'-endo 4.18 4.66 19.23
63 C A.C63 -62.0 167.3 50.9 80.7 -152.3 -70.7 -82(BI) -152.6(anti) 10.7(C3'-endo) ~C3'-endo 4.32 4.62 23.62
64 A A.A64 -66.9 180.0 44.1 75.8 -147.5 -76.5 -71(BI) -161.8(anti) 12.9(C3'-endo) ~C3'-endo 4.68 4.86 25.64
65 G A.G65 -44.0 164.2 49.9 79.8 -152.0 -73.3 -79(BI) -172.8(anti) 16.5(C3'-endo) ~C3'-endo 4.92 4.76 25.20
66 A A.A66 -57.9 178.5 52.0 81.7 -151.0 -73.5 -77(BI) -164.9(anti) 22.5(C3'-endo) ~C3'-endo 4.56 4.60 22.73
67 A A.A67 -62.0 164.1 54.2 83.2 -152.2 -78.3 -74(BI) -162.8(anti) 15.0(C3'-endo) ~C3'-endo 4.71 4.67 23.30
68 U A.U68 -59.8 175.3 47.3 82.2 -152.9 -65.4 -88(BI) -160.1(anti) 11.2(C3'-endo) ~C3'-endo 4.30 4.60 24.35
69 U A.U69 -63.8 168.1 55.1 79.1 -155.4 -85.6 -70(BI) -161.4(anti) 14.7(C3'-endo) ~C3'-endo 4.55 4.61 19.23
70 C A.C70 -61.7 164.6 53.1 79.0 -158.5 -64.5 -94(BI) -152.0(anti) 15.0(C3'-endo) ~C3'-endo 4.20 4.56 20.96
71 G A.G71 -78.4 173.6 60.3 80.3 -149.6 -68.4 -81(BI) -162.8(anti) 13.5(C3'-endo) ~C3'-endo 4.50 4.71 22.80
72 C A.C72 -73.2 176.2 62.1 83.0 -152.3 -67.9 -84(BI) -161.6(anti) 19.5(C3'-endo) ~C3'-endo 4.56 4.63 26.14
73 A A.A73 -63.3 177.7 50.4 81.6 -148.2 -66.1 -82(BI) -167.4(anti) 15.0(C3'-endo) ~C3'-endo 4.65 4.71 26.33
74 C A.C74 -66.9 -174.9 50.7 85.9 -145.0 -58.8 -86(BI) -153.1(anti) 11.8(C3'-endo) ~C3'-endo 4.22 4.61 33.45
75 C A.C75 -52.3 175.7 42.3 85.6 -131.9 163.9 64(BII) -151.7(anti) 15.1(C3'-endo) ~C3'-endo 3.96 4.60 159.78
76 A A.A76 -71.0 130.2 164.6 160.9 --- --- --- 138.5(anti) 176.1(C2'-endo) ~C2'-endo --- --- ---
******************************************************************************************
Virtual eta/theta torsion angles:
eta: C4'(i-1)-P(i)-C4'(i)-P(i+1)
theta: P(i)-C4'(i)-P(i+1)-C4'(i+1)
[Ref: Olson (1980): "Configurational statistics of polynucleotide chains.
An updated virtual bond model to treat effects of base stacking."
Macromolecules, 13(3):721-728]
eta': C1'(i-1)-P(i)-C1'(i)-P(i+1)
theta': P(i)-C1'(i)-P(i+1)-C1'(i+1)
[Ref: Keating et al. (2011): "A new way to see RNA." Quarterly Reviews
of Biophysics, 44(4):433-466]
eta": base(i-1)-P(i)-base(i)-P(i+1)
theta": P(i)-base(i)-P(i+1)-base(i+1)
nt eta theta eta' theta' eta" theta"
1 G A.G1 --- -139.3 --- -136.5 --- -110.8
2 C A.C2 171.9 -144.6 -175.5 -144.1 -136.1 -118.1
3 G A.G3 160.2 -151.4 173.9 -153.9 -145.0 -143.7
4 G A.G4 164.3 -144.6 177.7 -144.1 -154.8 -98.7
5 A A.A5 166.9 -138.1 -178.3 -135.8 -116.3 -111.6
6 U A.U6 172.1 -149.7 -170.8 -143.9 -130.1 -126.5
7 U A.U7 -158.0 -42.7 -138.7 -60.7 -120.5 -31.5
8 U A.U8 162.7 160.7 -159.9 -163.8 -142.6 176.2
9 A A.A9 -140.6 -38.9 -159.3 -112.7 157.1 -105.5
10 g A.2MG10 27.8 -130.3 97.2 -130.1 134.8 -110.3
11 C A.C11 170.3 -135.8 -175.7 -136.7 -137.8 -119.9
12 U A.U12 159.9 -121.6 176.5 -130.6 -148.5 -101.4
13 C A.C13 178.1 -179.1 -166.8 176.7 -118.5 178.4
14 A A.A14 171.9 -146.5 172.1 -133.4 -179.7 -74.6
15 G A.G15 164.3 -177.9 -166.6 -161.0 -92.6 -101.8
16 u A.H2U16 -124.1 -77.5 -114.2 -108.3 -72.5 -127.0
17 u A.H2U17 -10.5 -64.3 7.7 -94.7 17.3 -125.4
18 G A.G18 -21.0 -167.4 45.3 -160.9 61.3 -124.2
19 G A.G19 -127.4 -43.3 -122.0 -72.9 -105.8 -7.8
20 G A.G20 165.3 -100.4 -160.4 -101.1 -177.9 -115.4
21 A A.A21 -78.3 152.7 -68.0 155.1 -61.1 154.8
22 G A.G22 159.5 167.6 156.6 178.8 157.1 -162.6
23 A A.A23 178.4 -141.8 -173.5 -141.2 -156.1 -112.0
24 G A.G24 163.7 -139.5 177.7 -137.6 -137.6 -103.8
25 C A.C25 161.4 -132.6 179.2 -131.0 -128.2 -89.0
26 g A.M2G26 173.0 -133.0 -167.7 -130.4 -106.9 -93.6
27 C A.C27 163.5 -142.3 -178.0 -141.5 -123.6 -105.6
28 C A.C28 157.5 -143.8 171.1 -144.3 -136.3 -125.5
29 A A.A29 163.5 -152.9 179.0 -150.8 -142.9 -124.7
30 G A.G30 178.3 -127.8 -167.7 -126.5 -128.2 -72.5
31 A A.A31 165.4 -133.9 -174.3 -131.0 -101.0 -93.9
32 c A.OMC32 164.5 -139.2 -175.9 -138.0 -122.3 -108.9
33 U A.U33 165.1 -114.0 177.8 -158.5 -141.1 138.3
34 g A.OMG34 27.3 -121.7 50.5 -123.7 22.7 -84.4
35 A A.A35 162.5 -127.7 -177.7 -128.5 -116.8 -113.4
36 A A.A36 164.9 -172.7 -174.4 -169.2 -142.3 -115.1
37 g A.YYG37 163.1 -135.2 174.1 -131.3 -119.8 -79.8
38 A A.A38 170.2 -133.9 -173.3 -129.0 -104.3 -105.5
39 P A.PSU39 174.0 -132.6 -168.6 -131.2 -127.5 -89.6
40 c A.5MC40 163.1 -148.5 -177.6 -149.3 -115.9 -131.7
41 U A.U41 169.4 -148.8 177.2 -144.0 -152.9 -120.5
42 G A.G42 171.2 -150.4 -171.5 -151.6 -133.9 -124.5
43 G A.G43 174.2 -151.6 -174.4 -150.0 -134.0 -124.5
44 A A.A44 173.2 -120.4 -171.8 -120.0 -133.3 -72.6
45 G A.G45 168.6 -141.6 -168.3 -128.4 -103.4 -133.4
46 g A.7MG46 -143.2 -107.3 -133.6 -149.6 -148.2 -162.7
47 U A.U47 -31.5 -56.8 4.8 -91.0 24.9 -110.7
48 C A.C48 -82.5 53.9 -29.3 17.5 1.5 -107.6
49 c A.5MC49 -56.7 -145.3 -36.6 -142.8 103.2 -130.2
50 U A.U50 174.8 -146.6 -176.9 -142.8 -153.6 -113.8
51 G A.G51 170.3 -147.3 -175.5 -148.2 -134.2 -122.1
52 U A.U52 160.3 -145.8 173.9 -144.3 -141.8 -119.6
53 G A.G53 174.9 -141.5 -167.2 -142.4 -124.7 -111.6
54 t A.5MU54 171.1 -129.2 -177.4 -122.6 -133.3 -76.4
55 P A.PSU55 165.3 -115.2 -173.6 -155.4 -112.1 145.1
56 C A.C56 31.4 -126.9 51.6 -124.1 25.3 -87.4
57 G A.G57 164.3 -142.5 -174.1 -131.9 -119.2 -113.8
58 a A.1MA58 -131.5 -108.7 -105.3 -171.2 -104.2 159.8
59 U A.U59 1.8 -119.4 26.8 -109.9 49.0 -56.9
60 C A.C60 -171.8 -40.7 -130.1 -68.5 -70.2 -35.8
61 C A.C61 122.4 -148.3 168.6 -144.1 -158.2 -117.4
62 A A.A62 173.0 -146.6 -176.9 -144.9 -142.0 -119.6
63 C A.C63 164.5 -148.3 177.9 -149.6 -143.9 -128.6
64 A A.A64 158.4 -151.0 168.5 -148.2 -154.8 -122.8
65 G A.G65 173.6 -147.3 -172.0 -145.4 -130.5 -121.2
66 A A.A66 177.6 -145.4 -170.1 -142.7 -133.5 -111.9
67 A A.A67 165.6 -149.3 -176.9 -149.8 -129.8 -126.7
68 U A.U68 168.9 -138.2 179.4 -136.1 -143.2 -96.5
69 U A.U69 165.6 -160.5 -176.0 -161.2 -118.8 -156.9
70 C A.C70 166.7 -146.2 173.6 -149.0 -171.6 -127.0
71 G A.G71 161.0 -143.0 174.0 -142.3 -146.3 -113.4
72 C A.C72 166.1 -141.5 -177.5 -141.9 -131.5 -110.2
73 A A.A73 167.6 -137.8 -177.2 -133.3 -127.1 -89.8
74 C A.C74 171.2 -122.1 -172.8 -116.5 -116.2 -72.1
75 C A.C75 174.9 106.5 -161.9 109.8 -102.9 -139.3
76 A A.A76 --- --- --- --- --- ---
******************************************************************************************
Sugar conformational parameters:
v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'
tm: the amplitude of pucker
P: the phase angle of pseudorotation
[Ref: Altona & Sundaralingam (1972): "Conformational analysis
of the sugar ring in nucleosides and nucleotides. A new
description using the concept of pseudorotation."
J Am Chem Soc, 94(23):8205-8212]
nt v0 v1 v2 v3 v4 tm P Puckering
1 G A.G1 1.7 -23.4 35.1 -35.2 21.1 36.5 16.1 C3'-endo
2 C A.C2 1.6 -23.2 34.8 -34.8 20.9 36.2 16.1 C3'-endo
3 G A.G3 2.7 -25.1 36.8 -36.1 21.2 38.1 14.6 C3'-endo
4 G A.G4 -1.6 -22.3 36.3 -38.2 25.0 38.8 20.8 C3'-endo
5 A A.A5 10.1 -32.6 41.5 -36.6 16.7 41.7 4.8 C3'-endo
6 U A.U6 0.3 -24.0 37.3 -38.1 23.9 39.2 18.2 C3'-endo
7 U A.U7 -24.4 35.4 -32.4 18.9 3.3 35.4 156.1 C2'-endo
8 U A.U8 5.8 -28.7 39.7 -37.2 19.7 40.4 10.5 C3'-endo
9 A A.A9 -31.7 41.8 -35.6 18.1 8.4 41.2 149.8 C2'-endo
10 g A.2MG10 7.8 -28.0 36.7 -33.0 15.9 37.0 6.6 C3'-endo
11 C A.C11 1.2 -21.2 32.1 -32.5 19.8 33.5 16.8 C3'-endo
12 U A.U12 -4.6 -19.3 34.5 -37.9 26.7 38.1 25.2 C3'-endo
13 C A.C13 -3.4 -19.4 33.8 -36.4 25.1 36.9 23.7 C3'-endo
14 A A.A14 12.6 -30.8 36.8 -30.2 11.0 36.8 358.9 C2'-exo
15 G A.G15 1.9 -24.6 36.8 -36.8 22.2 38.3 16.0 C3'-endo
16 u A.H2U16 0.0 -18.7 29.2 -30.2 19.2 30.9 18.8 C3'-endo
17 u A.H2U17 23.0 -36.7 35.1 -23.2 0.2 37.0 341.4 C2'-exo
18 G A.G18 -27.9 39.5 -35.0 20.2 4.8 38.9 154.3 C2'-endo
19 G A.G19 -17.6 31.0 -31.9 23.1 -3.8 32.7 167.6 C2'-endo
20 G A.G20 6.6 -27.8 36.6 -34.2 17.5 37.0 8.7 C3'-endo
21 A A.A21 3.8 -25.0 35.1 -34.4 19.4 36.0 13.0 C3'-endo
22 G A.G22 16.4 -34.1 38.1 -29.5 8.3 38.3 353.8 C2'-exo
23 A A.A23 4.2 -26.6 37.4 -36.5 20.1 38.3 12.6 C3'-endo
24 G A.G24 3.9 -28.4 40.3 -39.3 22.4 41.5 13.4 C3'-endo
25 C A.C25 0.6 -24.5 37.8 -38.0 23.6 39.6 17.4 C3'-endo
26 g A.M2G26 6.3 -27.5 37.1 -34.7 17.9 37.6 9.3 C3'-endo
27 C A.C27 0.2 -23.5 36.5 -37.2 23.6 38.4 18.3 C3'-endo
28 C A.C28 6.6 -29.0 39.1 -36.3 18.8 39.6 9.2 C3'-endo
29 A A.A29 3.4 -26.6 38.4 -37.4 21.4 39.5 13.7 C3'-endo
30 G A.G30 2.6 -24.2 35.7 -34.9 20.4 36.9 14.5 C3'-endo
31 A A.A31 2.6 -24.0 35.0 -34.6 20.2 36.2 14.6 C3'-endo
32 c A.OMC32 -1.2 -21.7 35.1 -36.7 23.9 37.4 20.4 C3'-endo
33 U A.U33 3.5 -25.4 36.5 -35.3 20.1 37.5 13.3 C3'-endo
34 g A.OMG34 3.9 -22.7 32.2 -30.8 17.1 32.9 12.2 C3'-endo
35 A A.A35 -2.0 -19.9 32.7 -34.9 23.4 35.2 21.9 C3'-endo
36 A A.A36 -20.6 -7.3 30.6 -43.2 40.5 43.9 45.8 C4'-exo
37 g A.YYG37 2.1 -24.1 36.0 -35.6 21.0 37.4 15.4 C3'-endo
38 A A.A38 10.9 -30.3 37.6 -32.5 13.6 37.7 2.4 C3'-endo
39 P A.PSU39 2.1 -25.6 38.5 -38.4 22.8 40.0 15.8 C3'-endo
40 c A.5MC40 0.8 -22.5 34.6 -35.0 21.5 36.3 17.3 C3'-endo
41 U A.U41 3.8 -27.7 39.9 -38.6 22.0 41.0 13.4 C3'-endo
42 G A.G42 -1.7 -22.4 36.8 -38.6 25.4 39.4 20.9 C3'-endo
43 G A.G43 4.3 -27.6 39.1 -37.6 21.1 40.1 12.6 C3'-endo
44 A A.A44 1.0 -23.0 35.2 -35.4 21.6 36.8 16.9 C3'-endo
45 G A.G45 2.1 -24.3 35.7 -35.4 21.2 37.0 15.4 C3'-endo
46 g A.7MG46 -27.4 38.6 -34.7 19.7 4.7 38.5 154.5 C2'-endo
47 U A.U47 -20.9 34.8 -35.1 24.3 -2.2 36.4 164.9 C2'-endo
48 C A.C48 -25.6 38.4 -35.6 22.1 2.1 38.4 158.2 C2'-endo
49 c A.5MC49 5.8 -28.1 38.7 -36.0 19.1 39.3 10.1 C3'-endo
50 U A.U50 9.4 -32.2 41.0 -36.4 17.6 41.2 5.6 C3'-endo
51 G A.G51 4.9 -27.9 38.9 -36.8 20.3 39.7 11.5 C3'-endo
52 U A.U52 3.2 -28.5 41.4 -40.1 23.6 42.7 14.1 C3'-endo
53 G A.G53 -1.0 -23.1 37.0 -38.3 24.9 39.4 19.8 C3'-endo
54 t A.5MU54 -1.4 -22.2 35.9 -37.7 24.8 38.3 20.6 C3'-endo
55 P A.PSU55 6.2 -29.9 40.9 -38.3 20.4 41.5 10.1 C3'-endo
56 C A.C56 3.8 -25.3 35.7 -34.5 19.2 36.6 12.6 C3'-endo
57 G A.G57 4.0 -26.7 37.9 -36.5 20.6 38.9 12.8 C3'-endo
58 a A.1MA58 -24.3 38.4 -36.9 23.9 0.2 39.0 161.1 C2'-endo
59 U A.U59 -4.4 -18.3 31.8 -35.7 25.4 35.3 25.8 C3'-endo
60 C A.C60 -28.8 40.5 -36.4 21.2 4.7 40.3 154.8 C2'-endo
61 C A.C61 2.6 -25.5 36.8 -36.6 21.5 38.1 14.8 C3'-endo
62 A A.A62 5.9 -27.8 38.1 -35.4 18.8 38.7 9.9 C3'-endo
63 C A.C63 5.4 -27.3 37.5 -35.5 19.1 38.1 10.7 C3'-endo
64 A A.A64 4.1 -28.6 40.2 -38.8 22.2 41.2 12.9 C3'-endo
65 G A.G65 1.5 -26.6 39.5 -39.9 24.3 41.2 16.5 C3'-endo
66 A A.A66 -2.9 -21.6 36.5 -38.8 26.5 39.5 22.5 C3'-endo
67 A A.A67 2.4 -24.9 36.5 -36.1 21.4 37.8 15.0 C3'-endo
68 U A.U68 5.3 -28.4 39.5 -37.5 20.3 40.3 11.2 C3'-endo
69 U A.U69 2.9 -26.3 38.3 -37.9 22.3 39.6 14.7 C3'-endo
70 C A.C70 2.4 -25.9 38.7 -37.9 22.4 40.1 15.0 C3'-endo
71 G A.G71 3.7 -27.4 39.2 -38.3 21.8 40.3 13.5 C3'-endo
72 C A.C72 -0.6 -21.9 34.9 -36.2 23.1 37.0 19.5 C3'-endo
73 A A.A73 2.4 -25.4 37.3 -36.9 21.8 38.6 15.0 C3'-endo
74 C A.C74 4.4 -25.4 35.6 -34.0 18.6 36.4 11.8 C3'-endo
75 C A.C75 2.3 -22.5 33.1 -33.0 19.2 34.3 15.1 C3'-endo
76 A A.A76 -13.6 30.5 -34.8 27.7 -9.1 34.8 176.1 C2'-endo
******************************************************************************************
Assignment of sugar-phosphate backbone suites
bin: name of the 12 bins based on [delta(i-1), delta, gamma], where
delta(i-1) and delta can be either 3 (for C3'-endo sugar) or 2
(for C2'-endo) and gamma can be p/t/m (for gauche+/trans/gauche-
conformations, respectively) (2x2x3=12 combinations: 33p, 33t,
... 22m); 'inc' refers to incomplete cases (i.e., with missing
torsions), and 'trig' to triages (i.e., with torsion angle
outliers)
cluster: 2-char suite name, for one of 53 reported clusters (46
certain and 7 wannabes), '__' for incomplete cases, and
'!!' for outliers
suiteness: measure of conformer-match quality (low to high in range 0 to 1)
[Ref: Richardson et al. (2008): "RNA backbone: consensus all-angle
conformers and modular string nomenclature (an RNA Ontology
Consortium contribution)." RNA, 14(3):465-481]
nt bin cluster suiteness
1 G A.G1 inc __ 0
2 C A.C2 33p 1a 0.935
3 G A.G3 33p 1a 0.868
4 G A.G4 33p 1a 0.842
5 A A.A5 33p 1a 0.847
6 U A.U6 33p 1a 0.664
7 U A.U7 32p 1b 0.803
8 U A.U8 23p 2a 0.509
9 A A.A9 32p 1[ 0.046
10 g A.2MG10 23p 2g 0.640
11 C A.C11 33p 1a 0.507
12 U A.U12 33p 1a 0.898
13 C A.C13 33t 1c 0.824
14 A A.A14 trig !! 0
15 G A.G15 33p 1a 0.484
16 u A.H2U16 trig !! 0
17 u A.H2U17 33t !! 0
18 G A.G18 32p 5p 0.026
19 G A.G19 22p 4b 0.512
20 G A.G20 23p 2a 0.623
21 A A.A21 33t !! 0
22 G A.G22 33t 1f 0.714
23 A A.A23 33p 1a 0.840
24 G A.G24 33p 1a 0.881
25 C A.C25 33p 1a 0.967
26 g A.M2G26 33p 1a 0.819
27 C A.C27 33p 1a 0.698
28 C A.C28 33p 1a 0.923
29 A A.A29 33p 1a 0.973
30 G A.G30 33p 1a 0.838
31 A A.A31 33p 1a 0.914
32 c A.OMC32 33p 1a 0.782
33 U A.U33 33p 1a 0.897
34 g A.OMG34 33p 1g 0.784
35 A A.A35 33p 1a 0.517
36 A A.A36 33p 1a 0.670
37 g A.YYG37 33p 1a 0.625
38 A A.A38 33p 1a 0.903
39 P A.PSU39 33p 1a 0.680
40 c A.5MC40 33p 1a 0.942
41 U A.U41 33p 1a 0.945
42 G A.G42 33p 1a 0.630
43 G A.G43 33p 1a 0.882
44 A A.A44 33p 1a 0.837
45 G A.G45 33p 1a 0.749
46 g A.7MG46 32p 1[ 0.849
47 U A.U47 22p 4p 0.589
48 C A.C48 22t 2u 0.283
49 c A.5MC49 23p 6d 0.520
50 U A.U50 33p 1a 0.656
51 G A.G51 33p 1a 0.981
52 U A.U52 33p 1a 0.945
53 G A.G53 33p 1a 0.896
54 t A.5MU54 33p 1a 0.720
55 P A.PSU55 33p 1a 0.586
56 C A.C56 33p 1g 0.894
57 G A.G57 33p 1a 0.837
58 a A.1MA58 32p 1[ 0.332
59 U A.U59 23p 4d 0.411
60 C A.C60 32p 1b 0.662
61 C A.C61 23p 2a 0.553
62 A A.A62 33p 1a 0.895
63 C A.C63 33p 1a 0.964
64 A A.A64 33p 1a 0.791
65 G A.G65 33p 1a 0.586
66 A A.A66 33p 1a 0.940
67 A A.A67 33p 1a 0.941
68 U A.U68 33p 1a 0.891
69 U A.U69 33p 1a 0.951
70 C A.C70 33p 1a 0.809
71 G A.G71 33p 1a 0.761
72 C A.C72 33p 1a 0.832
73 A A.A73 33p 1a 0.965
74 C A.C74 33p 1a 0.886
75 C A.C75 33p 1a 0.639
76 A A.A76 32t !! 0
Concatenated suite string per chain. To avoid confusion of lower case
modified nucleotide name (e.g., 'a') with suite cluster (e.g., '1a'),
use --suite-delimiter to add delimiters (matched '()' by default).
1 A RNA nts=76 G1aC1aG1aG1aA1aU1bU2aU1[A2gg1aC1aU1cC!!A1aG!!u!!u5pG4bG2aG!!A1fG1aA1aG1aC1ag1aC1aC1aA1aG1aA1ac1aU1gg1aA1aA1ag1aA1aP1ac1aU1aG1aG1aA1aG1[g4pU2uC6dc1aU1aG1aU1aG1at1aP1gC1aG1[a4dU1bC2aC1aA1aC1aA1aG1aA1aA1aU1aU1aC1aG1aC1aA1aC1aC!!A
It gives me great pleasure to announce that the 3DNA/DSSR project is now funded by the NIH R24GM153869 grant, titled "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids". I am deeply grateful for the opportunity to continue working on a project that has basically defined who I am. It was a tough time during the funding gap over the past few years. Nevertheless, I have experienced and learned a lot, and witnessed miracles enabled by enthusiastic users.
Since late 2020 when I lost my R01 grant, DSSR has been licensed by the Columbia Technology Ventures (CTV). I appreciate the numerous users (including big pharma) who purchased a DSSR Pro License or a DSSR Basic paid License. Thanks to the NIH R24GM153869 grant, we are pleased to provide DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing" on the CTV landing page. Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu, copying xiangjun@x3dna.org.
DSSR v2.4.5-2024sep24 was released to synchronize with the new R24 funding, which will bring the project to an entirely new level. All existing users are encouraged to upgrade their installation to this release which contains miscellaneous bug fixes (e.g., chain id with > 4 chars) and numerous minor improvements.
Lots of exciting things will happen for the project. The first thing is to make DSSR freely accessible to the academic community. In the past couple of weeks, CTV have already issued quite a few DSSR Basic Academic licenses to users from all over the world. So the demand is high, and it will become stronger as more academic users become aware of DSSR. I'm closely monitoring the 3DNA Forum, and is always ready to answer users questions.
I am committed to making DSSR a brand that stands for quality and value. By virtue of its unmatched functionality, usability, and support, DSSR saves users a substantial amount of time and effort when compared to other options. My track record throughout the years has unambiguously demonstrated my dedication to this solid software product.
DSSR Basic contains all features described in the three DSSR-related papers, and includes the originally separate SNAP program (still unpublished) for analyzing DNA/RNA-protein complexes. The Pro version integrates the classic 3DNA functionality, plus advanced modeling routines, with email/Zoom/phone support.
