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RNA structures (DSSR) / Re: Delineating the components of bulges, internal loops, junctions, etc
« on: June 10, 2013, 05:46:13 pm »
Looks great, makes it much easier read!
Thanks
Thanks
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QuoteLet me ask around the lab and get their input and I'll make a suggestion based on what they suggest that would be most "user-friendly" and easily readable.That's great -- once I get your feedbacks, I will implement them in the next beta release of DSSR. I'm planning to add some new features to DSSR, including detection of kink-turns, but would take priority on refinements of existing functionality.Quote55 asymmetric internal loop: 7 nts; [1x2]; linked by [#168, #169]I like your idea for internal loop. Maybe stem loop, bulge, and junctions can follow the same pattern?
1 loop bases [A]; 0.G2855+(0.A2856)+0.C2857 [G(A)C]
2 loop bases [CA]; 0.G2900+(0.C2901+0.A2902)+0.C2903 [G(CA)C]
Xiang-Jun
55 asymmetric internal loop: 7 nts; [1x2]; linked by [#168, #169]
1 loop bases 0.A2856 [A]; 0.G2855+0.A2856+0.C2857 [GAC]
2 loop bases 0.C2901+0.A2902 [CA]; 0.G2900+0.C2901+0.A2902+0.C2903 [GCAC]
20 3-way junctions: 12 nts; [1x1x4]; linked by [#138, #-43, #140]
1 junction bases 0.U2330 [U]; 0.C2329+0.U2330+0.C2331+0 [CUC]
1 junction bases 0.A2356 [A]; 0.G2355+0.A2356+0.G2357 [GAG]
4 junction bases 0.A2367+0.A2368+0.A2369+0.A2370 [AAAA]; 0.C2366+0.A2367+0.A2368+0.A2369+0.A2370+0.G2371 [CAAAAG]
Thanks for the consideration!
Thanks for your feedback. As always, the more, the merrier! DSSR is currently in beta, and I am fully open to user suggestions for every aspect of the software, including format changes.
In writing DSSR, I came across many basic concepts in the literature of RNA structures that are well-known, yet not clearly defined (at least to my understanding). I tried to follow the conventions (where exist) as much as practical, and came up with my own 'ways' where necessary. It is my hope that DSSR would help in establishing pragmatic ways in charactering RNA (secondary) structures.
For your example case:Code: [Select]List of 12 bulge(s)
1 bulge: 6 nts; [2x0]; linked by [#19, #-8]
0.C245+0.G246+0.A247+0.A248+0.U265+0.G266 [CGAAUG]
It means that DSSR detects 12 bulges in the structure (1s72). For each bulge, DSSR outputs its type as a special case of internal loops with one strand containing 0 nts. Here the first bulge contains 2 nts, so of type [2x0]. Plus two enclosing canonical bps (here from stem #19, and lone bp #-8), the loop contains 6 nts (2+2+2). The listing below contains the 6 nts in sequential order, as would be obvious if one extracts just the nts and displayed them in Jmol or PyMOL. Here the two bulged out nts are 0.G246+0.A247.
I see your point for making components of the loop explicit, and will consider to implement extra output fields in future release of DSSR.
Xiang-Jun
Thanks for your kind words about DSSR.QuoteSeparating by chars vs. integers would be okay, but some alt. residues have numbers in them which makes it more difficult.Could you provide some specific cases to make your point clearer?
Xiang-Jun
1 4-way junction loop: 16 nts; [2x1x5x0]; linked by [#1, #2, #3, #4]
T.G7+T.U8+T.A9+T.G10+T.C25+T.A26+T.C27+T.G43+T.G44+T.G45+T.G46+T.G47+T.C48+T.G49+T.U65+T.C66 [GUAGCACGGGGGCGUC]
----Processing: 1BDN -------
total number of multiplets: 0
Uncaught exception 'Assertion failed' raised at [fncs_helix.c:911]
aborting...
Time used: 00:00:00:01
----Processing: 1QP5 -------
total number of multiplets: 0
total number of helices: 1
total number of stems: 1
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:01
----Processing: 1VTD -------
total number of multiplets: 0
total number of helices: 1
total number of stems: 1
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:00
----Processing: 2J00 -------
total number of multiplets: 108
total number of helices: 68
total number of stems: 101
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:16
----Processing: 2J02 -------
total number of multiplets: 106
total number of helices: 67
total number of stems: 98
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:16
----Processing: 2ZJR -------
total number of multiplets: 170
total number of helices: 117
total number of stems: 180
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:19
----Processing: 3OHK -------
A.G1332 0.10
A.A2346 0.10
total number of multiplets: 218
total number of helices: 108
total number of stems: 177
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:13
----Processing: 3OHZ -------
A.A2346 0.11
total number of multiplets: 208
total number of helices: 111
total number of stems: 178
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:13
----Processing: 3OI0 -------
total number of multiplets: 88
total number of helices: 63
total number of stems: 89
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:20
Found no basepairs for: 3OI0
----Processing: 3OI1 -------
total number of multiplets: 210
total number of helices: 112
total number of stems: 178
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...
Time used: 00:00:00:12
----Processing: 6CRO -------
total number of multiplets: 0
Uncaught exception 'Assertion failed' raised at [fncs_helix.c:911]
aborting...
Time used: 00:00:00:01
--------------PDB ID: 1N3E --------------
total number of helices: 1
total number of stems: 6
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:215]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 1QCU --------------
total number of helices: 10
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:191]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 1QLN --------------
total number of helices: 2
total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 1Y26 --------------
total number of helices: 5
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:191]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2DLC --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2GCV --------------
total number of helices: 5
total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2H0S --------------
total number of helices: 5
total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2H0W --------------
total number of helices: 5
total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2NZ4 --------------
Residue [E.G1] has canonical ring atoms missed (8 vs 9)
total number of helices: 22
total number of stems: 40
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2PXB --------------
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2PXD --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXE --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXF --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXK --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXL --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXP --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXQ --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXT --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXU --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXV --------------
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2V3C --------------
N.G215 0.10
total number of helices: 6
total number of stems: 13
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2VJU --------------
total number of helices: 4
total number of stems: 6
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2XM3 --------------
total number of helices: 12
total number of stems: 18
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2XMA --------------
total number of helices: 8
total number of stems: 12
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2XO6 --------------
total number of helices: 6
total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2XQC --------------
total number of helices: 6
total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2ZUE --------------
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2ZUF --------------
total number of helices: 3
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3ADD --------------
total number of helices: 6
total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3AGV --------------
total number of helices: 4
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3AM1 --------------
total number of helices: 3
total number of stems: 6
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3C1B --------------
total number of helices: 4
total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:02
-------------------------------------
--------------PDB ID: 3CC2 --------------
total number of helices: 106
total number of stems: 179
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:08
-------------------------------------
--------------PDB ID: 3DD2 --------------
total number of helices: 2
total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3EGZ --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3FOZ --------------
total number of helices: 5
total number of stems: 9
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3H8X --------------
Residue [C.DA279] has canonical ring atoms missed (8 vs 9)
total number of helices: 2
total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3HAX --------------
F.FHU7 0.16
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3HJW --------------
E.FHU10 0.15
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3HXO --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3LQX --------------
total number of helices: 2
total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3LWP --------------
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3LWR --------------
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3LWV --------------
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3MNN --------------
atom 12042: [RU@F.RU2001] has > 6 bonds
atom 12068: [RU@G.RU2001] has > 6 bonds
atom 12094: [RU@H.RU2001] has > 6 bonds
total number of helices: 5
total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:02
-------------------------------------
--------------PDB ID: 3MXH --------------
total number of helices: 4
total number of stems: 7
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3RW6 --------------
H.CCC62 0.10
F.CCC62 0.10
total number of helices: 4
total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3U4M --------------
total number of helices: 4
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3U56 --------------
total number of helices: 4
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3UMY --------------
total number of helices: 4
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3UTB --------------
total number of helices: 2
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3ZGZ --------------
total number of helices: 6
total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4AQ7 --------------
total number of helices: 6
total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 4ARC --------------
total number of helices: 3
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4ARI --------------
total number of helices: 4
total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4AS1 --------------
total number of helices: 3
total number of stems: 5
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4ATO --------------
total number of helices: 1
total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 4HQU --------------
total number of helices: 2
total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4HQX --------------
total number of helices: 3
total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...
Time used: 00:00:00:00
-------------------------------------
Thanks for your feedback.
Just to be sure: by ".outp", you mean the option "find_pair -p"-generated file "allpairs.ana" which is then fed into "analyze"? How about the default setting? i.e., the ".out" file?
I will think more about this request, and I may come up with something. If I decide to go for it, I'd output the B-factor average/occupancy for any input structure, not just crystal structures. Moreover, there would be a new command line option for such info, which is OFF by default to be compatible with previous 3DNA releases.
To help me help you in this endeavor, could you provide (at least) a concrete example with the values you want?
Xiang-Jun
Hi,
As far as I understand such information is obtained by parsing PDB files and 3DNA output using an (afaik) unpublished python parser called X3DNA-Parser by Yurong Xin.
You can find her e-mail address at:
http://epigenomics.columbia.edu/wordpress/?page_id=6
Perhaps you can drop her a line. I remember vaguely that perhaps she had a UML diagram of the parser in her PhD thesis.
Cheers,
M.
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.