Messages

1051

RNA structures (DSSR) / A bug with missing right-side type bulges

« on: December 25, 2013, 07:29:36 pm »

This thread is to replace the original one titled "an issue with bulges" stared by febos. Somehow, the URL with the original thread does not reflect the topic, and trying to fix the issue leads to a broken link when clicking directly on the topic subject. [Note added on 2014-01-10: the broken URL bug has been fixed.]

The original thread with three posts is still kept for record, and this new thread is a direct copy of the original posts.

Xiang-Jun

1052

RNA structures (DSSR) / Re: an issue with bulges

« on: December 25, 2013, 03:00:25 pm »

Hi Eugene,

The missing right-type bulges bug has been fixed in DSSR beta-r28-on-20131225. Please have a try and report back how it goes.

For PDB entry 1ffk, chain 9, the corresponding output section now looks like below:

Code: [Select]

****************************************************************************
List of 2 hairpin loop(s)
   1 nts=4 GCGA closed by pair {9.C89+9.G94 [CG], #8}
       9.C89+9.G90+9.C91+9.G92+9.A93+9.G94 [CGCGAG]
   2 nts=5 AUCCC closed by pair {9.C37+9.G43 [CG], #-1}
       9.C37+9.A38+9.U39+9.C40+9.C41+9.C42+9.G43 [CAUCCCG]

****************************************************************************
List of 3 bulge(s)
   1 bulge: 5 nts; [0x1]; linked by [#2, #3]
       9.C15+9.G16+9.C64+9.A65+9.G66 [CGCAG]
       0 nts bulge ; 9.C15-->9.G16 [CG]
       1 nts bulge 9.A65 [A]; 9.C64-->9.G66 [CAG]
   2 bulge: 6 nts; [0x2]; linked by [#4, #5]
       9.C29+9.C30+9.G50+9.A51+9.A52+9.G53 [CCGAAG]
       0 nts bulge ; 9.C29-->9.C30 [CC]
       2 nts bulge 9.A51+9.A52 [AA]; 9.G50-->9.G53 [GAAG]
   3 bulge: 5 nts; [1x0]; linked by [#7, #8]
       9.G86+9.U87+9.G88+9.C95+9.C96 [GUGCC]
       1 nts bulge 9.U87 [U]; 9.G86-->9.G88 [GUG]
       0 nts bulge ; 9.C95-->9.C96 [CC]

****************************************************************************
List of 3 internal loop(s)
   1 asymmetric internal loop: 14 nts; [6x4]; linked by [#3, #4]
       9.G21+9.G22+9.U23+9.U24+9.G25+9.C26+9.C27+9.U28+9.A54+9.U55+9.A56+9.A57+9.G58+9.C59 [GGUUGCCUAUAAGC]
       6 nts iloop 9.G22+9.U23+9.U24+9.G25+9.C26+9.C27 [GUUGCC]; 9.G21-->9.U28 [GGUUGCCU]
       4 nts iloop 9.U55+9.A56+9.A57+9.G58 [UAAG]; 9.A54-->9.C59 [AUAAGC]
   2 symmetric internal loop: 10 nts; [3x3]; linked by [#5, #-1]
       9.U33+9.A34+9.C35+9.C36+9.C37+9.G43+9.A44+9.A45+9.C46+9.A47 [UACCCGAACA]
       3 nts iloop 9.A34+9.C35+9.C36 [ACC]; 9.U33-->9.C37 [UACCC]
       3 nts iloop 9.A44+9.A45+9.C46 [AAC]; 9.G43-->9.A47 [GAACA]
   3 asymmetric internal loop: 13 nts; [5x4]; linked by [#6, #7]
       9.G75+9.G76+9.A77+9.G78+9.U79+9.A80+9.C81+9.G101+9.G102+9.A103+9.A104+9.A105+9.C106 [GGAGUACGGAAAC]
       5 nts iloop 9.G76+9.A77+9.G78+9.U79+9.A80 [GAGUA]; 9.G75-->9.C81 [GGAGUAC]
       4 nts iloop 9.G102+9.A103+9.A104+9.A105 [GAAA]; 9.G101-->9.C106 [GGAAAC]

****************************************************************************
List of 1 junction(s)
   1 3-way junctions: 16 nts; [4x3x3]; linked by [#1, #2, #6]
       9.C9+9.C10+9.A11+9.C12+9.A13+9.G14+9.C67+9.G68+9.U69+9.U70+9.C71+9.G110+9.U111+9.U112+9.C113+9.G114 [CCACAGCGUUCGUUCG]
       4 nts junction 9.C10+9.A11+9.C12+9.A13 [CACA]; 9.C9-->9.G14 [CCACAG]
       3 nts junction 9.G68+9.U69+9.U70 [GUU]; 9.C67-->9.C71 [CGUUC]
       3 nts junction 9.U111+9.U112+9.C113 [UUC]; 9.G110-->9.G114 [GUUCG]

****************************************************************************
List of 2 non-loop single-stranded segment(s)
   1 nts=3 9.U1-->9.A3 [UUA]
   2 nts=3 9.A120-->9.C122 [ACC]

Again, thanks for reporting the bug!

Xiang-Jun

1053

RNA structures (DSSR) / Re: an issue with bulges

« on: December 24, 2013, 11:30:20 am »

Hi Eugene,

Thanks for reporting the bulging issue. Your example (PDB id 1ffk, chain 9) clearly illustrates a bug in DSSR for detecting bulges. The nts missed in right bulges are classified as single-stranded. So the two manifestations are of the same origin.

Over the past couple of weeks, I've actually been thinking about tidying up the algorithm for identifying the various loops and presenting them consistently. Your bug report fits just in time. I will try to fix the issue soon.

Best regards,

Xiang-Jun

1054

MD simulations / Re: dna torsional angle wheels

« on: December 14, 2013, 11:37:55 am »

Hi Ara,

The torsion wheel images you referred to look very nice and compact. You may need to contact to original author (or the PI) of the figures for further details. In the meantime, have a look of the thread "How to make a nice visualization for angle distribution?".

Xiang-Jun

1055

General discussions (Q&As) / Re: How to calculate Bending?

« on: December 12, 2013, 09:11:28 am »

Does the corresponding entry How to calculate DNA bending angle? help? Searching the Forum will lead you to more discussions on this topic.

You may also want to try Curves/Curves+.

Xiang-Jun

1056

General discussions (Q&As) / Re: determining helical pitch of curved DNA

« on: December 10, 2013, 03:18:36 pm »

I wonder if there are plans to implement such a property for calculation in 3DNA?

In principle, I'd be interested in implementing such a property in 3DNA. To that end, I need direct access to details: either a worked example, or a working program with sample input and output files. Pure text descriptions or mathematical formula as often seen in scientific publications help for general understanding, but they are certainly not enough from a programatic point of view.

Xiang-Jun

1057

General discussions (Q&As) / Re: determining helical pitch of curved DNA

« on: December 05, 2013, 12:14:18 pm »

Hi Alexey,

Thanks for using 3DNA and posting your questions on the Forum.

It has been speculated for quite some time, that the DNA in nucleosomes is over twisted (approx. 10 bp per turn instead of 10.5), so I want to show this using 3DNA analysis. An intuitive way to get the value of average helical pitch would be summing the values of twist returned by 3DNA along the DNA and dividing by the number of base pairs. However, I'm not quite sure if this approach is rigorous, and whether one should sum up the values of helical twist of dimer step twist. What do you think?

I am aware of the paper "Helical repeat of DNA in solution" by Wang (PNAS 1979) where it was found that "Analysis of the set ... gives the DNA helix repeat in solution as 10.4 base pairs per turn under physiological conditions, with an estimated probable error of +/- 0.1." The "twist" measurement here is an average of covalently closed DNAs. In my understanding, it is related to linker number and writhe, but differs from the dinucleotide-step twist angles from 3DNA. See "Two perspectives on the twist of DNA" by Tobias et al. However, why not pursue your "intuitive way" further to see what you can get. It won't take much time, and the result (whatever it could be) would be informative.

2) During MD simulations some base pairs might become distorted and they are not found by find_pairs. I can force the calculations on them by manually editing .inp file, however, I assume that the Twist, Roll, Tilt values reported for the base pair steps would be arbitrary.
Will the summation of all twist angles along the DNA helix be meaningful in this case in order to obtain overall twist of the DNA helix?

Two points here. Regarding the issues of 'local' vs 'overall' twist, see above. Distorted base-pairs do not have "arbitrary" step parameters: they are derived based on the geometry given in a PDB/mmCIF input file, and can be used to 'rigorously' rebuild the original base pairs. More generally, the default cutoffs in 3DNA are a good starting point. However, there are always boundary cases where the choice is sort of arbitrary. For example, the vertical separation (stagger) is 2.5 Å by default. So a dinucleotide step with a value of 2.49 Å would satisfy this criterion, whereas 2.51 Å won't.

HTH,

Xiang-Jun
 

1058

RNA structures (DSSR) / Re: Bug report of DSSR beta

« on: December 03, 2013, 03:24:30 pm »

Hi Eugene,

The bug has been fixed in DSSR beta-r27-on-20131203. Now the output looks like below:

Code: [Select]

        bp1_pars:  [-1.59    0.32     -0.26    1.95     -3.60    -43.73]
       step_pars:  [2.96     -1.31    3.22     -5.29    6.77     34.80]
       heli_pars:  [-3.00    -5.49    2.46     11.10    8.68     35.82]
        bp2_pars:  [-2.37    -0.60    0.11     4.67     -7.75    -2.95]
Please have a try, and keep reporting back any bugs you may find!

Thanks,

Xiang-Jun

1059

RNA structures (DSSR) / Re: Bug report of DSSR beta

« on: December 03, 2013, 09:21:35 am »

Hi Eugene,

Good catch. I will get it fixed in the next beta release soon.

Thanks,

Xiang-Jun

1060

General discussions (Q&As) / Re: Finding base pair having a overlap

« on: December 03, 2013, 12:00:38 am »

Hi Chan Gu,

Thanks for posting two PDB files and an image, which help clarify the issues. Firstly, I'd say that you are certainly on the extreme side for some bp-defining parameters (e.g., H-bond distance cutoff of 20 Å). I am glad to see that 'find_pair' is still working properly, without giving many extraneous bps. Secondly, to force a pair between DA5/1 and DT3/60, you could simply edit the default output file as below:

From:
    2         # duplex
   29         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    2   59  0 #    1 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<....  1.88  1.82 46.49  8.64  2.83

****************************************************************************
To:
    2         # duplex
   30         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   60
    2   59  0 #    1 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<....  1.88  1.82 46.49  8.64  2.83

As shown clearly in your attach image, DA5/1 and DT3/60 are stacking instead of pairing. In such extreme cases, 'find_pair' does not work as you'd expect, for solid reasons. Here certain manual editing is required, as illustrated above. I take this 'extra work' as an advantage since it reminds users to pay attentions to the abnormality.

If you are analyzing MD trajectories for an ensemble of similar structures, you do not need to run 'find_pair' for each model. See x3dna_ensemble analyze -h for further info.

HTH,

Xiang-Jun

1061

General discussions (Q&As) / Re: Finding base pair having a overlap

« on: December 02, 2013, 07:18:04 am »

Could you please post a specific example? The defaults in 3DNA/DSSR have been set the way they are for solid reasons, and work well for the vast majority of cases.

Xiang-Jun

1062

General discussions (Q&As) / Re: Problem of finding all base pairs in distorted DNA structure using 3DNA

« on: November 28, 2013, 10:07:49 pm »

What 'same problem' do you have? As shown in Difei's last post on this thread, his problem has been solved.

Please start a new topic, and be specific with your problem by providing a reproducible example.

Xiang-Jun

1063

RNA structures (DSSR) / Re: Non-standard alternate location indicator

« on: November 28, 2013, 10:36:01 am »

Hi Eugene,

The issues you experienced with 406D.pdb2 etc are due to the non-standard "Alternate location indicator" at column 17 in PDB format. By default, 3DNA/DSSR treats only the standard variants, "A1 ", i.e., when the column #17 character is either " " (space), "A", or "1". For 406D.pdb2, the alternate location indicator on column #17 is "B", as shown below:

Code: [Select]

ATOM      6  O3'B  C A   1      -3.349  35.281  69.551  1.00  9.66           O 
ATOM      7  C2'B  C A   1      -2.839  34.367  67.344  1.00  9.66           C 
ATOM      8  O2'B  C A   1      -4.232  34.217  67.145  1.00  9.66           O 
ATOM      9  C1'B  C A   1      -2.214  35.046  66.123  1.00  9.66           C 
ATOM     10  N1 B  C A   1      -0.760  34.826  66.025  1.00  8.90           N 
ATOM     11  C2 B  C A   1      -0.276  33.554  65.677  1.00  8.90           C 
ATOM     12  O2 B  C A   1      -1.094  32.628  65.441  1.00  8.90           O 

In this case, you need to run DSSR by specifying the --altloc=B option:

Code: [Select]

x3dna-dssr -i=406D.pdb2 --altloc=B
The same rule applies to other entries you listed. Of course, you need to specify the altloc character for each case specifically. Note that for 406D.pdb3, you should add the --altloc=C option as well to get the desired result. The " " (space) altloc is always checked.

It is interesting to note that PDB is handling x-ray crystal structures with MODEL/ENDMDL, and altloc this way. The REMARK 200 in the PDB entry 406d may be helpful.

Code: [Select]

REMARK 200 REMARK: THE CRYSTAL PACKING OF 17-BP RNA DUPLEX IS STATICALLY       
REMARK 200  DISORDERED. AS A RESULT, THE ASYMMETRIC UNIT OF THE CRYSTAL         
REMARK 200  CONTAINS FOUR SUPERIMPOSED ORIENTATIONS OF THE DUPLEX THAT ARE     
REMARK 200  OUT OF REGISTER, SUCH THAT BACKBONES SUPERIMPOSE, BUT BASE         
REMARK 200  IDENTITY DIFFERS.
HTH,

Xiang-Jun

1064

Users' contributions / Re: DNA conformational energy components

« on: November 25, 2013, 01:58:57 pm »

Thanks for posting you question on the 3DNA Forum, and I am glad to see that you have solved your own problem.

As its name implies, the "Users' contributions" section is not part of the 3DNA distribution. It is made possible and maintained (if any) by enthusiastic users like you.

Thanks,

Xiang-Jun

1065

General discussions (Q&As) / Re: Zp parameter A/vs B DNA

« on: November 23, 2013, 03:06:06 pm »

Thanks for the two references.

Xiang-Jun

1066

General discussions (Q&As) / Re: Zp parameter A/vs B DNA

« on: November 23, 2013, 12:16:49 pm »

Hi Amedeo,

It should be possible, at leat in principle,  to classify a single strand as A, B, AB or whatever, although strong irregularities are to be expected.

I agree with you on this point. It is logical to imagine that each of the two single-strand dinucleotides in an A-form double-helical step would have A-like conformation; similar argument holds for the B-form.

Indeed  I have found an example in the literature where even the ss-5'-AAA-3' trimer in solution has been characterized as B-DNA by using  2D-NMR and molecular dynamics simulations.

Could you provide the reference?

I have not found crystallographic structures of ss-oligonucleotides, but I am not a crystallographer, hence a sligthly off-topic question: « are you aware of examples of "pure" ss-DNA crystals, i.e. without proteins, ligands, etc.? »

I do not have an example at hand. However, I believe a search of the NDB should help.

Xiang-Jun

1067

General discussions (Q&As) / Re: Zp parameter A/vs B DNA

« on: November 21, 2013, 02:13:28 pm »

I don't think you would want to classify a single strand as A or B, only a double-strand.

Thanks for chiming in. Could you please eleborate on your point?

As a follow-up to my previous reply, I've written a post titled "Single- and double-stranded Zp" to clarify the naming confusion.

Xiang-Jun

1068

RNA structures (DSSR) / Re: what does helix-form mean?

« on: November 21, 2013, 02:06:59 pm »

Hi Eugene,

DSSR classifies each double-helical dinucleotide step into a helix-form of A/B/Z/./x, standing for A-form, B-form, Z-form, undecided (.), or with backbone breaks (x), respectively.

Code: [Select]

            123456789012
strand-1 5'-GACGGACAAGUU-3'
 bp-type    |||...|||||.
strand-2 3'-CUGAAAGUUCGA-5'
helix-form  A...xx.AAAx
In the above example, the strand-1 row gives base sequence in 5' to 3' direction, and the strand-2 row corresponds to the pairing sequence in 3' to 5' direction. The bp-type row has a symbol of '|' for each canonical pair  (Watson-Crick or wobble), and '.' otherwise. The helix-form row has number-of-base – 1 terms, corresponding to the number of dinucleotide steps, and the last column is alway empty. Here the first dinucleotide step, GA/UC, is classified as A-form. The following three steps have proper backbone linkage, but cannot be assigned to A-, B- or Z-form, thus '.'. The fifth step, GA/AA, has backbone break(s), thus 'x'. The following steps have similar meanings.

The method used in DSSR for classifying a double-helical step into A-, B-, or Z-form is experimental, and more details will be reported later. It's worth noting that the method is different from the Zp-based one used in the original 3DNA analyze program.

THT,

Xiang-Jun

1069

RNA structures (DSSR) / Re: a little note about DSSR installation

« on: November 19, 2013, 08:49:55 am »

Hi,

Thanks for your follow up. Your method means another way to run DSSR on native Windows, i.e. with a copy of Cygwin1.dll and the Cygwin complied version of DSSR. I think (untested) that you could also put DSSR under the $X3DNA/bin directory, so you do not need to copy Cygwin1.dll around. As long as you can run other 3DNA commands, DSSR also should work just fine.

Best regards,

Xiang-Jun

1070

General discussions (Q&As) / Re: Zp parameter A/vs B DNA

« on: November 18, 2013, 02:00:21 pm »

While I was posting my previous reply, you guys have come up with another round of exchange on the topic. Very impressive...THANK YOU!

The single-stranded Zp was not intended as a classifier for A- vs B-DNA as noted in my previous reply. I did see the confusion here, and I will write a post with more info on this topic shortly. In the meantime, please continue to report your suggestions, findings, etc.

Xiang-Jun

1071

General discussions (Q&As) / Re: Zp parameter A/vs B DNA

« on: November 18, 2013, 01:50:03 pm »

Thank you, Amedeo, for posting such swell-thought-out question regarding Zp vs A/B-DNA classification. Thank you, Mauricio, for your quick response which answers Amedeo's question per the 3DNA NAR03 paper and the paper titled "A-form conformational motifs in ligand-bound DNA structures".

Amedeo's question prompted me to think deeper on the Zp parameter for single-stranded vs double-stranded DNA/RNA structures. The Zp value calculated with the analyze -torsion treats the input structure as single-stranded by expressing the 3'-phosphorus on the reference frame of the preceding base, while the default Zp is for a double-stranded structure as defined in the above two papers. The 1.5 Å cut-off refers to the double-stranded Zp, which is an average of the z-coordinates of the two 'middle' phosphorus atoms in the middle step frame.

The single-stranded Zp was introduced mostly as a more robust substitute than the Richardson Dp parameter to characterize C2'-endo vs C3'-endo sugar puckering. Note that here the cut-off is 2.9 Å. See my post "Sugar pucker correlates with phosphorus-base distance".

To the best of my knowledge, Zp is the most discriminative parameter to classify A- vs B-DNA (duplex). It also helps to check other parameters, such as slide, and x-displacement etc.

HTH,

Xiang-Jun

1072

RNA structures (DSSR) / Re: a little note about DSSR installation

« on: November 16, 2013, 08:40:52 am »

Hi Eugene,

Thanks for using DSSR and reporting back your findings on running the Cygwin version under native Windows environment. Did you install Cygwin and run the DSSR Cygwin version in that environment? Does DSSR run as expected there?

If you want to run DSSR directly under native Windows, the DSSR MinGW version is the way to go. See my post titled "DSSR works perfectly under DOS (in native Windows)". Please have a try, and report back how it goes.

DSSR is meant to be minimalistic, self-contained, without reliance on third-party libraries. Users just need to install the right version. I am interested in seeing counterexamples, and would take proper actions to ensure that DSSR is indeed self-contained.

HTH,

Xiang-Jun

1073

General discussions (Q&As) / Re: generating 10.5 bp/turn B-DNA

« on: November 11, 2013, 11:04:02 am »

Also regarding PHENIX, I never used that before. Actually I need to use this rebuilt structure for AMBER simulations so before molecular dynamics I will perform minimization with AMBER which should take care of geometric concerns. Do you still think that I should use PHENIX before AMBER minimization?

A nice feature about the PHENIX-restraint optimization is that one can fix the base geometry, and minimize the sugar-phosphate backbone only. AMBER should be perfectly fine, it is just that I do not know how to do it in detail. It helps if you could summarize the procedure for the benefit of other 3DNA/AMBER users.

Good luck!

Xiang-Jun

1074

General discussions (Q&As) / Re: generating 10.5 bp/turn B-DNA

« on: November 10, 2013, 09:13:34 pm »

Hi Jiomm,

Thanks for using 3DNA (w3DNA) and posting your questions on the Forum. The procedure you outlined sounds fine to me. Note that with the 3DNA rebuild program, you can generate an arbitrary structure with any prescribed sequence and associated base-pair and step (or helical) parameters. Since the process is rigorous and reversible, you will get the same parameters back if you analyze the generated structure. It is up to the user to decide whether the structure is meaningful in a particular context.

For your case, you could simply reset twist from 36 degrees to 34.29, while keeping other parameters fixed. I do not understand your rationale of changing rise from 3.37 Å to 3.5385 [i.e., the formula 3.37+ (3.37/2)/10 = 3.5385]. With your settings, the helical pitch is larger than the fiber B-DNA model.

Also note the rebuild structure may have irregular sugar-phosphate backbone connectivity, which can be 'regularized' with restraint optimization using PHENIX.

HTH,

Xiang-Jun

1075

RNA structures (DSSR) / DSSR release history

« on: October 31, 2013, 11:24:21 am »

As the list is becoming quite long, for easy reference, I have split up the DSSR release notes from the main post "DSSR: Dissecting the Spatial Structure of RNA". DSSR may be licensed from the Columbia Technology Ventures (CTV).

DSSR v2.8.1-2026mar12
Release notes since R24 funding

V1.x releases

• v1.9.10-2020apr23 -- added the nt_type field (with values "DNA", "RNA", or "unknown") to the nts array of JSON output, plus many code refactoring and feature revisions on DSSR-PyMOL schematics.
• v1.9.9-2020feb06 -- Added the --nt-mapping option so users can specify how modified nucleotides are mapped to their canonical counterparts. Please refer to the thread "modified nucleotides incorrect" initiated by tctcab on the 3DNA Forum. This update also contains many refinements at the DSSR-PyMOL interface for producing the characteristic block schematics. See http://skmatic.x3dna.org.
• v1.9.8-2019oct16 -- Added the --g4-onz option for ONZ classifications of G-tetrads in intramolecular G-quadruplexes, plus minor code refinements.
• v1.9.7-2019oct01 -- Fixed a bug in the identification of junction loops in special cases (as in PDB entry: 4wsm) -- thanks to lijun for reporting.
• v1.9.6-2019sep16 -- Revised the --get-hbond option, plus miscellaneous code/manual refinements.
• v1.9.5-2019aug01 -- Checked the compatibility of the --symm option with an NMR-ensemble-like input file where only the first model is handled; enhanced features on the analysis and output of G-quadruplexes; revised identification of duplex-G4 junctions (e.g., in 6r9k/6r9l).
• v1.9.4-2019jul08 -- Revised criteria for Watston-Crick pairs and improved identification of loops in rare cases. Updated the DSSR User Manual, which is now at 108 pages. Miscellaneous code refinements.
• v1.9.3-2019may25 -- Refined the code for command-line options; Added --block-opt (or --block-option) as an alternative for --block-file.
• v1.9.2-2019may06 -- Revised the algorithm for the alignment of G-tetrads along a G-helix. Now the left-handed G-quadruplex 6fq2 has a Twist angle of -25.8 degrees; Plus other minor code refinements.
• v1.9.1-2019apr06 -- Revised the --analyze-cehs option so that for non-WC structures it gives consistent results with the cehs program in 3DNA v2.4; added the output of a set of six "Simple helical parameters based on consecutive C1'-C1' vectors" with the --analyze option.
• v1.9.0-2019mar26 -- Added the --analyze option to output a list of key structural parameters as those from the 3DNA v2.x ‘analyze’ program. This option can also be specified as --3dna-v2, and it contains variations to fit other potential needs.

• v1.8.9-2019mar09 -- Revised algorithms for the identificaton of modified nucleotides, multiplets, and loops, in edge cases; expanded the definition of ~rHoogsteen pairs (e.g., G2-G12 in PDB entry 6ac7).
• v1.8.8-2019feb18 -- Relaxed criteria for reverse Hoogsteen (rHoogsteen) pairs; revised the algorithm for base identification in special cases.
• v1.8.7-2019feb11 -- Refined code and fixed a couple of bugs in rare occasions.
• v1.8.6-2019feb03 -- Refined the algorithm for H-bonds, plus documentation improvements and code refactoring.
• v1.8.5-2018nov29 -- Fixed the bug of not escaping backslash and double quote in DSSR JSON output.
• v1.8.4-2018nov12 -- (1) Further refinements of G-tetrad reference frame, leading to slightly revised twist angle. (2) Updated examples in command-line help text. (2) A few other minor revisions.
• v1.8.3-2018oct29 -- (1) Replaced raw C1' atomic coordinates with least-squares-fitted ones in the definition of G-tetrad reference frames. This switch ameliorates experimental uncertainty of C1' atomic coordinates, and is in line with the usage of the origins of G reference frames. As a result, helical parameters (Twist, Rise etc.) are slightly different from previously reported values. (2) Add a descriptive note for G4 stems that incorporates common names (including chair, basket, hybrid) and strand directionality, as in note=basket(2+2) for PDB id 2kf8. (3) Introduced a squared G-tetrad block of size 11.6 Å for visualization. (4) Added the --pair-only option to output just base-pairing info, which is 10 times faster than a default DSSR run. (5) Tightened the criteria of G-U Wobble pair. Now the U2586-G2592 pair in PDB id 1s72 is named ~Wobble. The pair has a Shear in the opposite direction of a normal Wobble pair, with two completely different H-bonds: N3(imino)*N2(amino)[3.05],O4(carbonyl)-N1(imino)[2.77]
• v1.8.2-2018oct20 -- Added detection of V-loops in G-quadruplexes, plus miscellaneous improvements.
• v1.8.1-2018oct09 -- Further refinements and expansions on the characterization of G-quadruplexes. (1) Added support of a consistent topological nomenclature for canonical G4 structures; (2) revised the algorithm for identifying G4 loops to allow for 0-nt propeller loop as in PDB entry 2m53; (3) recovered the missing G6+G10 pair in a distorted G-tetrad in PDB entry 148d; (4) implemented full JSON output of G4 structural features. DSSR is now full-fledged for the analysis and annotation of G-quadruplexes.
• v1.8.0-2018sep18 -- Significantly improved the characterization of G-quadruplexes, (1) revised the algorithm for the calculation of G-tetrad step parameters (twist/rise); (2) new features for the assignment of groove widths (medium, narrow, or wide), classification of stacking interactions based on the two faces of G-tetrads, and categorization of higher-order associations (coaxial stacking). Other refinements related to the identification of base-pairs and multiplets.

• v1.7.9-2018sep06 -- sped up further the analysis of NMR ensembles or MD trajectories; revised algorithms for identifying base pairs and multiplets in special cases; improved the mmCIF parser; plus minor code/manual refinements.
• v1.7.8-2018sep01 -- classified G-tetrads by different types of non-planarity; sped up analyses of large ensembles (--nmr) as the trajectories from MD simulations; introduced the "Linker" G+A base-pair name/type; revised the algorithm for H-bonding identification, plus numerous other minor code refactoring and refinements.
• v1.7.7-2018apr20 -- revised detection of multiplets in edge cases; miscellaneous minor refinements.
• v1.7.6-2018mar22 -- significantly refactored code for running multiple instances of DSSR in parallel; introduced the --auxfile=no option to bypass the generation of the auxiliary files; added three FAQ entries and a section on DSSR integrations to the manual.
• v1.7.5-2018mar19 -- revised code associated with the --blocview option for generating cartoon-block schematic images using PyMOL, in the most extended view; minor but fixes and code improvements.
• v1.7.4-2018jan30 -- revised the algorithm for H-bond detection, plus other minor code/manual improvements.
• v1.7.3-2017dec26 -- revised the JSON output of model/chain keys for consistency; incorporated abasic sites into analysis by default; revised code to avoid warning messages with GCC v7.
• v1.7.2-2017nov20 -- fixed a bug with abasic sites (as in PDB entry 4ifd, with --abasic), and a bug in the listing of modified nucleotides (as in PDB entry 2c4z in its biological assembly, with --symm); a variety of minor enhancements  of source code and the documentation.
• v1.7.1-2017nov01 -- fixed a bug in the analysis of G4-quadruplexes in rare cases; revised the characterization of i-motifs; checked this release on all nucleic-acid-containing structures in the PDB.
• v1.7.0-2017oct19 -- added a module to automatically identify and fully characterize G-quadruplexes, plus numerous other internal code refinements.

• v1.6.9-2017aug09 -- refined algorithms for identifying H-bonds and base pairs for boundary cases, plus miscellaneous code factoring and revisions.
• v1.6.8-2017mar28 -- fixed a bug in loop identification in edge cases (as in 4fe5); expanded standard bases to include A5 and A3 etc; fixed the 1-unit shift bug in the concatenated backbone suite string; fixed a bug in chain-specific DBN (as in 5pky); revised base-pair criteria to include C.U4--D.U4 pair in 1zh5; extended criteria for type=X A-minor-like motifs (U49 to U20--A76 in 4fe5); checked for output of non-stacked bases independently of stacked ones (as in 4rts); miscellaneous code/manual refinements.
• v1.6.7-2017mar14 -- fixed a bug in derived dot-bracket notation (DBN) with pseudoknots in special cases; revised --json to work with --get-hbonds for a full list of all H-bonds (DSSR and SNAP); changed type=O to type=X for eXtended A-minor motifs to avoid confusion with the previously documented type 0; lowered the default angle for splayed-apart dinucleotides from 100 degrees to 85; miscellaneous code/documentation refinements. 
  
• v1.6.6-2017feb20 -- extended A-minor motifs to include a miscellaneous type other than I and II; added groove widths to helices/stems and sequential number to nts of the JSON output; updated the user manual.
• v1.6.5-2017jan22 -- revised detection of pairs and helices/stems in rare cases; miscellaneous minor refinements.
• v1.6.4-2016nov19 -- refined detection of multiplets; added the characterization of terminal bases of helices/stems in the 'Summary' section; revised Jmol-DSSR web interface.
• v1.6.3-2016oct19 -- added a new section of splayed-apart dinucleotides and larger units; plus miscellaneous code refinements and minor bug fixes.
• v1.6.2-2016sep19 -- refined the algorithm for identifying kink-turns (K-turns), among many other internal improvements.
• v1.6.1-2016aug22 -- added the identification and characterization of i-motifs (e.g., 1a83 and 2n89); refined algorithms for the identification of H-bonds and helices; miscellaneous code refactoring.
• v1.6.0-2016aug06 -- added the --pair-list option to allow for user customizations of base pairs to be analyzed; added an analysis of the global curvature for each nucleic acid chain; plus various code refinements.

• v1.5.9-2016jul22 -- further refinements of the algorithm for H-bonding detection.
• v1.5.8-2016jul09 -- added a 'summary' line for each loop, plus miscellaneous code refinements.
• v1.5.7-2016jun16 -- refined the algorithm for H-bonding detection in corner cases (such as G-tetrads with poor geometry).
• v1.5.6-2016jun09 -- revised the summary line of DNA/RNA chains when multiple models are involved; consolidated/extended cartoob-block related functionality; internal code refinements and minor bug fixes.
• v1.5.5-2016may25 -- added the --view option (and related variants) to reset a structure via the principle moment of inertia, as in rotate_mol of 3DNA. The output orientation is in the most extended form, vertically; --blocview (or --block-view, --cartoon-block-view) option is also accepted to mimic the 3DNA blocview script; simplified the command-line help/examble message, and revised the user manual accordingly.
• v1.5.4-2016may16 -- significantly refined and extended the --frame option to reorient a structure based on a selected reference frame, including the middle frame of two base-pair frames, as in frame_mol of 3DNA; added output of the suite string in dssr-torsions.txt; minor bug fixed and refinements; updated user manual.
• v1.5.3-2016apr11 -- derived a set of virtual torsion angles using the phosphorus atoms and base origins (see output file dssr-torsions.txt). This set of P-base virtual torsions was first implemented in analyze -torsion of 3DNA v2.1, released in early 2012. See my blogpost titled "Pseudo-torsions to simplify the representation of DNA/RNA backbone conformation" (dated 2012-04-22) for details. Moreover, functions related to the --block-color option have been refined.
• v1.5.2-2016apr02 -- added the --block-color option to facilitate flexible color customizations of blocks/edges (e.g. minor groove); expanded the definition of junction loops to include the special case of a kissing loop motif mediated by an isolated canonical pair (e.g., 1ehz); various minor internal refinements.
• v1.5.1-2016mar11 -- miscellaneous code refinements and function enhancements.
• v1.5.0-2016feb12 -- removed the obsolete --jmol option since the DSSR-Jmol integration is now better served via JSON; added more styles in the cartoon-block representation.

• v1.4.9-2016jan25 -- fixed inconsistency in the dot-bracket-notation (dbn) output section regarding chain names with more than 1-char (as for 1vy6 in .cif format) -- thanks to Eugene for reporting the bug; refined .r3d output of base blocks for PyMOL rendering, following feedback from Thomas Holder.
• v1.4.8-2016jan16 -- refined the definition of extended base-pair names ("~Wobble", "~Hoogsteen", "~rHoogsteen", and "~Shear"); fixed a bug in the identification of G quartets in rare cases.
• v1.4.7-2016jan06 -- extended definition of base-pair names, with "~Wobble", "~Hoogsteen", "~rHoogsteen", and "~Shear" for corresponding pairs with similar geometry but sequences other than G–U, A+U, A–U, G–A, respectively.
• v1.4.6-2015dec16 -- refined detection of H-bonds, base-pairs, multiplets, and helices/stems for boundary cases.
• v1.4.5-2015nov23 -- added the --nar-paper option for rigorously reproducing the results reported in the 2015 DSSR Nucleic Acids Research paper; miscellaneous code refinements.
• v1.4.4-2015nov18 -- refined detection of base-pairs and multiplets in boundary cases; made the output of base-capping interactions by default (i.e., the --more option is no longer needed to be specified for its output).
• v1.4.3-2015oct23 -- added detection of metallo-base pairs, such as T-Hg-T (4l24) and C-Ag-C (5ay2) from the work of Kondo et al.
• v1.4.2-2015oct19 -- revised code for circular DNA or RNA molecules and unconventional glycosidic linkages (such as C1'–C1 for DY).
• v1.4.1-2015oct12 -- checked for potential erroneous usage of option --symmetry with an NMR ensemble (which leads to DSSR effectively taking the models all together); revised output width of id strings.
• v1.4.0-2015oct10 -- introduced the --nmr option to facilitate processing of NMR ensembles or trajectories of molecular dynamics simulations; added a new section summarizing structural features per nucleotide. Up to this point, DSSR contains all the fundamental features I have had in mind!

• v1.3.9-2015oct08 -- simplified diagnostic message, and refactored code.
• v1.3.8-2015oct02 -- added option --cartoon-block, plus a few minor refinements.
• v1.3.7-2015oct01 -- added option --symmetry (short form: --symm) to take symmetry-related MODEL/ENDMDL ensemble as a whole. This option is useful for x-ray crystal structures where the asymmetric unit is 'half' of the biological unit (e.g., PDB id: 467d -- x3dna-dssr -i=467d.pdb1 --symm).
• v1.3.6-2015sep18 -- revised JSON output for better DSSR-Jmol integration (thanks to Dr. Robert Hanson). Specifically, a "metadata" property is introduced to collect miscellaneous information, thus simplifying the top-level name space. Moreover, "ntParams" is renamed "nts" for consistency.
• v1.3.5-2015sep09 -- bug fixes for edge cases in JSON output, based on tests against all nucleic acid structures in PDB; minor code refactoring. The DSSR JSON output has now reached a stable, useable state.
• v1.3.4-2015sep06 -- fixed a bug in parsing .cif files as in PDB entry 5aj0 (thanks to Eugene for reporting the issue).
• v1.3.3-2015sep03 -- added output of reference frames of bases and base-pairs in JSON, exposing more of DSSR's functionality to other third-party tools (e.g., for visualization).
• v1.3.2-2015sep02 -- introduced a new set of "simple" base-pair (bp) parameters that are more intuitive for non-canonical bps. The simple parameters, including Shear, Stretch, Buckle and Propeller, are for structural description only, not suitable for model rebuilding. The non-planarity bp parameters, Buckle and Propeller in particular, have recently received attention in the RNA structure community. This simple set of bp parameter is provided to make DSSR more readily accessible to X-ray crystallographers or cryo-EM practitioners. The new parameters complement, but not replace, the original six rigid-body bp parameters for rigorous description and exact rebuilding of nucleic acid structures.
  
  When the --more option is specified, the new parameters are available in the main output file, taking an extra line for each bp. For --non-pair, the inter-base angle and minimum distance between base atoms are also listed. The new additions break backward compatibility of the main output file; use the --nar-paper option to stay with DSSR v1.2, as reported in the NAR article. Better yet, users are strongly encouraged to switch to the JSON output format for better connection with DSSR.
  
  
• v1.3.1-2015aug29 -- revised tag names for the --json output based on feedback from Dr. Wilma Olson; along the line, changed the file name dssr-a2bases.pdb to dssr-atom2bases.pdb to make its meaning more explicit for atom over base capping interactions.
• v1.3.0-2015aug27 -- added option --json to collect all DSSR-derived structural features in the standard JSON data exchange format. This single JSON file makes DSSR results easily parsable, allowing for its seamless integration with other RNA bioinformatics tools. Plus various other minor refinements.

• v1.2.9-2015jul25 -- added a new section on Reproducing results published in the DSSR-NAR paper to the 3DNA Forum, and documented corresponding auxiliary options in the User Manual.
• v1.2.8-2015jun15 -- added a new section titled "Additional options" to the User Manual; refined the algorithm for hydration identification.
• v1.2.7-2015jun09 -- added documentation of two related options: --prefix to customize the prefix of DSSR auxiliary files, and --cleanup to remove those files; other minor changes.
• v1.2.6-2015mar28 -- revised the interpretation of DSSR to "Dissecting the Spatial Structure of RNA"; added a new option --loop-isolated-pair to exclude isolated canonical pairs in delineating loops; updated the user manual (now 60 pages).
• v1.2.5-2015mar19 -- revised the helix/stem detection algorithm for circular DNA/RNA structures.
• v1.2.4-2015mar03 -- refined the algorithm for assigning dot-bracket notation (dbn) in rare cases, plus miscellaneous minor improvements.
• v1.2.3-2015feb18 -- improved the identification of multiplets.
• v1.2.2-2015feb06 -- refined the algorithm for assigning helices, plus several code refactoring and enhancements.
• v1.2.1-2015feb01 -- added the functionality for the "characterization of H-type pseudoknots"; refined the underlying algorithms for identifying H-bonds and base pairs.
• v1.2.0-2015jan01 -- numerous code refinements and refactoring; added classification of base-stacking interactions (option --non-pair); introduced the helix index that an isolated canonical pair is part of; included metal coordination bonds that phosphate OP1/OP2 atoms are involved in (option --po4); replaced option --long-idstr with --idstr; made option --nested explicit; added a new section on base stacks.

• v1.1.10-2014nov04 -- refined the algorithm for identifying multiplets; expanded option --non-pair to include all non-pairing interactions; various minor improvements.
• v1.1.9-2014oct22 -- refined H-bond identification and significantly fine-tuned base pair classification; updated the user manual.
• v1.1.8-2014oct09 -- fixed a bug in assigning G+A pairs to Saenger type X (10); further refined algorithms for finding H-bonds and base pairs.
• v1.1.7-2014sep24 -- added auxiliary files (where available) dssr-bulges.pdb, dssr-iloops.pdb and dssr-junctions.pdb to parallel dssr-hairpins.pdb; further refined the algorithm for H-bond detection; significantly improved the User Manual -- by switching to LaTeX, all the hyperlinks and cross references are active, and the excerpted output listings in the manual are auto-synced with the latest DSSR release via a Ruby script.
• v1.1.6-2014sep09 -- refined algorithms for detecting H-bonding and base-stacking interactions; removed the 4-line header in .bpseq output; checked for chain breaks in pseudoknot report; various code polishing.
• v1.1.5-2014aug28 -- added the section of atom-base stacking interactions (as in the case of the phosphate OP2 atom of G57 capping over the uracil ring of PSU55 in tRNA "1ehz"); significantly sped up the --non-pair and --phosphate options; miscellaneous code refinements.
• v1.1.4-2014aug09 -- added the option --nest to remove pseudo-knots (if any), leaving only nested pairs; added a new section to list modified nucleotides; numerous minor refinements.
• v1.1.3-2014jun18 -- refined the algorithm for deriving dot-bracket notation (.dbn) in RNA structures with higher-order pseudo knots (thanks to Jan Hajic); added secondary structure output in .bpseq format to parallel .ct and .dbn; miscellaneous code improvements.
• v1.1.2-2014apr19 -- added the option --torsion360 to output (virtual) torsional angle in the range of [0, 360] instead of the default range [-180, +180], following Cathy Lawson's suggestion; renamed "00-n/a" to "n/a" for unclassified Saenger pairs, plus a few other refinements of the User Manual based on feedback from Pascal Auffinger; revised A-minor separator character from '/' to '|' (i.e., from 'A/G-C' to 'A|G-C') based on communications with Bob Hanson.
• v1.1.1-2014apr11 -- added the option --get-hbonds to find and output all H-bonds in a structure; renamed file ‘dssr-torsions.dat’ to ‘dssr-torsions.txt’; updated the User Manual (50 pages)
• v1.1.0-2014apr09 -- denoted unnamed bps as '--' for easy parsing (thanks to feedback from Dr. Robert Hanson); added helical radius info for helices/stems, and made the helical rise parameter explicit (thanks to Dr. Wilma Olson); changed '_pars' to '-pars' in the output file for consistency; upgraded DSSR to v1.1.0-2014apr09 due to format changes.

• v1.0.6-2014apr04 -- revised the algorithm for detecting kissing loops, plus other minor refinements; updated the User Manual accordingly.
• v1.0.5-2014mar24 -- removed the --note option which has become redundant with notes in the main output file and the DSSR User Manual; shortened output from the --help option by deleting the 'Summary' section; minor code refinements. Added the overlooked subsection "Orientation of helices/stems" and fixed a few typos and inconsistencies in the User Manual (48 pages).
• v1.0.4-2014mar19 -- minor updates on notes in the main output file to synchronize with an significantly improved DSSR User Manual (46 pages) based on feedback from Dr. Wilma Olson.
• v1.0.3-2014mar09 -- various improvements for consistency, and finally and most importantly, the DSSR User Manual (45 pages) is out!
• v1.0.2-2014feb16 -- numerous minor refinements, mostly as a result of writing up the DSSR User Manual (coming soon!).
• v1.0.1-2014jan31 -- Refined the algorithm for detecting multiplets [thanks to Eugene]; fixed a bug for handling circular DNA/RNA structures [thanks to Pascal]; plus consistency improvements.
• v1.0-2014jan25 -- The program is robust and mature enough to warrant a v1.0 release. While DSSR will be continuously refined, top priority will be on bug fixes. Wherever practical, future DSSR v1.x releases will remain backward compatible.

Beta-testing releases

• beta-r30-on-20140118 -- considerably improved annotation and consistency of the main DSSR output file with help from Dr. Wilma Olson, refined algorithms for detecting internal and junction loops, added output of secondary structures in the connect (.ct) format and the extended DBN notation to allow for multiple molecules or fragments, removed the --break-symbol option. This will be the last beta release, and shortly we will move to DSSR v1.0! Please give it a try and let me know anything you'd like to change!
• beta-r29-on-20140106 -- significantly improved the algorithms for detecting various loops (hairpin, bulge, internal or junction loops), covering many corner cases. List of nucleotides in loops and single-stranded fragments are now presented consistently. Plus many code refinements.
• beta-r28-on-20131225 -- fixed a bug for missing 0-by-N type (right-side) bulge (thanks to Eugene).
• beta-r27-on-20131203 -- added the missing bracket ([) to delineate base-pair parameters in detailed output for helices/stems (thanks to Eugene).
• beta-r26-on-20131128 -- code refinements and refactoring, plus minor bug fixes. Single-stranded fragments now refer to nucleotides not involved in loops or canonical base-pairs (Watson-Crick and G-U wobble); simplified idstr for the non-standard compliant yet commonly encountered PDB files (mostly from MD simulations) with no chain id specified, from e.g. _.G1 to G1.
• beta-r25-on-20131119 -- added option --break-symbol to delineate chain breaks in dot-bracket notation; listed terminal single-stranded segments; plus code refinements/refactoring.
• beta-r24-on-20131030 -- refined code for nucleotide characterization; annotated the Levitt pair.
• beta-r23-on-20130918 -- bug fixes on U-turn identification and missing base pairs.
• beta-r22-on-20130910 -- minor bug fixes and code refinements; released the DSSR web-interface.
• beta-r21-on-20130903 -- fixed a rare bug reported by Pascal, and refined the mmCIF parsing code.
• beta-r20-on-20130830 -- added option --u-turn to detect UNR- or GNRA-type U-turns, plus numerous code refinements.
• beta-r19-on-20130819 -- added option --po4 (--phosphate) to list H-bonds involving phosphate groups; removed the segid info from nucleotide id-string by default;  refined code internally and fixed minor bugs.
• beta-r18-on-20130801 -- added support for the mmCIF format; refined code for parsing the PDB format.
• beta-r17-on-20130723 -- assigned backbone suite names (in file "dssr-torsion.dat") following Richardson et al. "RNA backbone: consensus all-angle conformers and modular string nomenclature"; numerous code refinements and note revisions.
• beta-r16-on-20130709 -- classified each dinucleotide step into A-, B- or Z-form conformation; simplified output by default. Users are advised to upgrade to this release.
• beta-r15-on-20130703 -- added output of base morphology parameters for each identified helix/stem.
• beta-r14-on-20130626 -- auto-detection of 'canonical' kink-turns (k-turns) and reverse k-turns (see my post "DSSR identifies kink-turns!"); numerous code refinements.
• beta-r13-on-20130618 -- added the PDB segment identifier (segid) into nucleotide id string; refine the algorithm for finding A-minor motifs.
• beta-r12-on-20130610 -- delineated the components of bulges, internal loops, and junctions, per user request.
• beta-r11-on-20130603 -- refined the descriptive note with the help of Dr. Wilma Olson; added the --long-idstr option to explicitly delineate fields of a residue id string for easy machine parsing; added the --pucker option to output the sugar pucker following either Altona & Sundaralingam (1972) or Westhof & Sundaralingam (1983) -- see the post "Two slightly different definitions of sugar pucker".
• beta-r10-on-20130430 -- added a brief descriptive note and a list of generated files to the main DSSR output; revised the command-line --help with more detailed usage info; improved output format, and refined code. Now DSSR is not only self-contained, but also (at least should be) self-explanatory.
• beta-r09-on-20130421 -- added a least-squares fitted helical axis for each identified helix/stem; classified the backbone into BI/BII conformations and the sugar into C2'/C3'-endo like (see file 'dssr-torsions.dat'); checked for non-pairing interactions (H-bonds or base stacking) with option '-non-pair'; refined code and revised output format
• beta-r08-on-20130323 -- refined algorithm for multiplet detection, revised the header section to output the numbers of DNA/RNA chains, nucleotides, waters, and metals
• beta-r07-on-20130322 -- code refinements, minor bug fixes, and more extensive tests
• beta-r06-on-20130319 -- fixed the "segmentation fault" bug reported by MarcParisien for PDB entry 2a64; revised -h message
• beta-r05-on-20130316 -- detection of ribose zippers; revision of help message; code refactoring
• beta-r04-on-20130314 -- detection of kissing loops; output format revisions, including an explicit listing of all nucleotides involved in hairpin loops; internal bug fixes and refinements
• beta-r03-on-20130309 -- extensive tests against all RNA/DNA-containing structures in the PDB as of March 2013, bug fixes and refinements
• beta-r02-on-20130306 -- bug fixes, and internal improvements
• beta-r01-on-20130303 -- initial release