1
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
Q&As related to x3DNA-DSSR; an online community for DNA/RNA structural bioinformatics x3DNA-DSSR · w3DNA
Show Posts
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers
Pages: [1]
2
RNA structures (DSSR) / Re: Delineating the components of bulges, internal loops, junctions, etc
« on: June 07, 2013, 05:07:40 pm »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
Hi Xiang-Jun,
Thanks first for considering user input in to how the output is formatted.
I talked to a few involved with RNA, and the first thing they agreed upon was that the bulges, internal loops, junctions and (to a lesser extent) ribose zipper would benefit from being more explicit in which residues belonged to which strand or junction. More specifically, each strand/junction is on a separate line.
According to the input above, this slightly revised example for seems to be easy to understand for junctions/loops/bulges.
Code: [Select]
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!
3
RNA structures (DSSR) / Re: Delineating the components of bulges, internal loops, junctions, etc
« on: June 07, 2013, 01:35:07 pm »
Hi Xiang-Jun,
Let 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.
For internal loops, the same suggestion above would be nice, IE. for 1S72:
55 asymmetric internal loop: 7 nts; [1x2]; linked by [#168, #169]
0.G2855+0.A2856+0.C2857+0.G2900+0.C2901+0.A2902+0.C2903 [GACGCAC]
Would be readable as:
55 asymmetric internal loop: 7 nts; [1x2]; linked by [#168, #169]
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]
Thanks
Let 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.
For internal loops, the same suggestion above would be nice, IE. for 1S72:
55 asymmetric internal loop: 7 nts; [1x2]; linked by [#168, #169]
0.G2855+0.A2856+0.C2857+0.G2900+0.C2901+0.A2902+0.C2903 [GACGCAC]
Would be readable as:
55 asymmetric internal loop: 7 nts; [1x2]; linked by [#168, #169]
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]
Thanks
4
RNA structures (DSSR) / Re: Delineating the components of bulges, internal loops, junctions, etc
« on: June 07, 2013, 12:32:21 pm »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
Hi Xiang-Jun,
Thanks for the reply and clarification.
It makes sense, but when looking searching for a specific case (IE. a "flipped-out- adenosine in a bulge) it is not as straight-forward as it could be as one has to make inferences.
When talking to some RNA people in my lab about it and showing them the output, they were a bit confused as well at first as it was not explicitly delineated.
If I am quickly looking through a file for a 2-bulge, your program makes it imminently easy to find that. I just look for [2x0].
However, if one wants to go a step further and find a [2x0] containing a non-paired adenosine, it becomes a bit more difficult when reading a concatenated line like: 0.C245+0.G246+0.A247+0.A248+0.U265+0.G266
Thanks again
5
RNA structures (DSSR) / Delineating the components of bulges, internal loops, junctions, etc
« on: June 07, 2013, 10:40:50 am »
Hi again Xiang-Jun,
Hopefully you are not tired of my comments and suggestions by now!
I was recently looking through a couple RNA structures looking for a bulge with a non-paired adenosine
and found that it was quite difficult to discern what is what in bulges/internal loops/junctions
just by reading the list of residues. Meaning, which residues are on one strand or the complement, or which residue in a [1x0] bulge
are not paired, etc.
To give an example, a simple bulge from 1S72:
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]
As the residues are listed all on one line, it is not immediately apparent which residues are on which
strand and which 2 residues are "flipped out" without going in to the PDB and analyzing the structure.
Would there be any way to have the program show this distinction?
IE:
1 bulge: 6 nts; [2x0]; linked by [#19, #-8]
2 bulge bases [GA]; 0.C245+(0.G246+0.A247)+0.A248 [C(GA)A]
0 bulge bases; 0.U265+0.G266 [UG]
The same concept holds for internal loops and junctions, basically any structural element that uses the [AxB(xC)] nomenclature. It would, to a layman, make it
much simpler to analyze if the component strands and unpaired/mispaired residues were delineated in some way.
Perhaps I'm just not that well versed in RNA secondary structure vocabulary and the like, but I found it somewhat hard to discern this distinction without a bit more digging.
Thanks so much.
Hopefully you are not tired of my comments and suggestions by now!
I was recently looking through a couple RNA structures looking for a bulge with a non-paired adenosine
and found that it was quite difficult to discern what is what in bulges/internal loops/junctions
just by reading the list of residues. Meaning, which residues are on one strand or the complement, or which residue in a [1x0] bulge
are not paired, etc.
To give an example, a simple bulge from 1S72:
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]
As the residues are listed all on one line, it is not immediately apparent which residues are on which
strand and which 2 residues are "flipped out" without going in to the PDB and analyzing the structure.
Would there be any way to have the program show this distinction?
IE:
1 bulge: 6 nts; [2x0]; linked by [#19, #-8]
2 bulge bases [GA]; 0.C245+(0.G246+0.A247)+0.A248 [C(GA)A]
0 bulge bases; 0.U265+0.G266 [UG]
The same concept holds for internal loops and junctions, basically any structural element that uses the [AxB(xC)] nomenclature. It would, to a layman, make it
much simpler to analyze if the component strands and unpaired/mispaired residues were delineated in some way.
Perhaps I'm just not that well versed in RNA secondary structure vocabulary and the like, but I found it somewhat hard to discern this distinction without a bit more digging.
Thanks so much.
6
RNA structures (DSSR) / Re: Parsing the base pair identifiers - separating base type from base number
« on: June 07, 2013, 10:04:59 am »
Works great, thanks!
7
RNA structures (DSSR) / Re: Parsing the base pair identifiers - separating base type from base number
« on: May 31, 2013, 10:30:09 am »
Okay, a separate option would be nice, but I understand if that's not what you intend for the output.
An example from PDB 1D9H, you have a modified base U31 of residue number 16 on chain A.
DSSR displays it as "B.U31/16", separating the numeral in the base type from the numeral of the residue number. If they all took that format, it would be nice for those who wish to parse the DSSR data.
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
An example from PDB 1D9H, you have a modified base U31 of residue number 16 on chain A.
DSSR displays it as "B.U31/16", separating the numeral in the base type from the numeral of the residue number. If they all took that format, it would be nice for those who wish to parse the DSSR data.
8
RNA structures (DSSR) / Parsing the base pair identifiers - separating base type from base number
« on: May 30, 2013, 06:44:40 pm »
Hi again,
Great program, like all the improvements you've made so far.
Now, I'm trying to parse the output given by DSSR using Python, and so far it is quite easy. However, I'm running in to a bit of trouble when trying to parse the base identifiers.
IE. "0.C309" from 1S72, it is easy enough to split the strand from the base type/residue number, but then separating C from 309 becomes more difficult.
Separating by chars vs. integers would be okay, but some alt. residues have numbers in them which makes it more difficult.
Is there any way you would want to add another separator for base type from base number?
Ex. "0.C_309" or the like?
Thanks
Great program, like all the improvements you've made so far.
Now, I'm trying to parse the output given by DSSR using Python, and so far it is quite easy. However, I'm running in to a bit of trouble when trying to parse the base identifiers.
IE. "0.C309" from 1S72, it is easy enough to split the strand from the base type/residue number, but then separating C from 309 becomes more difficult.
Separating by chars vs. integers would be okay, but some alt. residues have numbers in them which makes it more difficult.
Is there any way you would want to add another separator for base type from base number?
Ex. "0.C_309" or the like?
Thanks
9
RNA structures (DSSR) / Re: DSSR - List of bases involved in hairpins?
« on: March 14, 2013, 07:57:31 pm »
That is amazing, thanks so much! Works like a charm.
Will let you know if I see anything amiss as I look at more and more secondary structures.
Will let you know if I see anything amiss as I look at more and more secondary structures.
10
RNA structures (DSSR) / DSSR - List of bases involved in hairpins?
« on: March 12, 2013, 06:21:24 pm »
Hi,
Really liking DSSR. I was wondering if there was any way you can have it expressly state the bases involved in the hairpins instead of implied by the closing base pair? The same way you do for 4-way junctions.
Really liking DSSR. I was wondering if there was any way you can have it expressly state the bases involved in the hairpins instead of implied by the closing base pair? The same way you do for 4-way junctions.
Quote
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]
11
RNA structures (DSSR) / Re: Bug report of DSSR beta
« on: March 09, 2013, 09:24:35 pm »
Thanks Xiang-Jun!
I definitely know the type of structures you are talking about. Pymol has a hard time processing them as well.
I definitely know the type of structures you are talking about. Pymol has a hard time processing them as well.
12
RNA structures (DSSR) / Re: Bug report of DSSR beta
« on: March 08, 2013, 04:33:52 pm »
Hi,
Thanks for fixing those bugs! Hope you don't mind if I bring you some more bugs with the revised version:
Thanks!
Thanks for fixing those bugs! Hope you don't mind if I bring you some more bugs with the revised version:
Code: [Select]
----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
Thanks!
13
RNA structures (DSSR) / Re: Bug report of DSSR beta
« on: March 04, 2013, 02:39:49 pm »
Hi xiangjun,
Caught a few C-exceptions on PDB's that should all have base pairs:
Caught a few C-exceptions on PDB's that should all have base pairs:
Code: [Select]
--------------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
-------------------------------------
14
RNA structures (DSSR) / Bug report of DSSR beta
« on: March 04, 2013, 01:59:44 pm »
Hi xiangjun,
Great program. Looks to find structural motifs really well.
I ran in to a bit of a problem though, DSSR seems to hang on 2VQE. BFactors.dat and the pairs.pdb files are generated, but the program just hangs thereafter. I've processed all the other large ribosome structures with no problems, but this one seems to give it a hard time. I've tried stdout and writing out, neither work.
I've tried re-downloading the PDB, as well. It works fine for 3DNA.
Thanks
Great program. Looks to find structural motifs really well.
I ran in to a bit of a problem though, DSSR seems to hang on 2VQE. BFactors.dat and the pairs.pdb files are generated, but the program just hangs thereafter. I've processed all the other large ribosome structures with no problems, but this one seems to give it a hard time. I've tried stdout and writing out, neither work.
I've tried re-downloading the PDB, as well. It works fine for 3DNA.
Thanks
15
General discussions (Q&As) / Re: B-Factor values from PDB in output files?
« on: February 13, 2013, 07:12:21 pm »
Either way would be great, thanks!
What will the output format for the new program look like? Will it be similar to 3DNA's?
Thanks
What will the output format for the new program look like? Will it be similar to 3DNA's?
Thanks
16
General discussions (Q&As) / Re: B-Factor values from PDB in output files?
« on: February 13, 2013, 05:01:19 pm »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,
Thanks so much for even considering this request!
I did not know the PDB even reported occupancy or temperature factor values for NMR/CryoEM structures.
I use .outp files because they tend to have all the base mispairs that the standard output fails to capture.
Command line is as you said:
>find_pair -p -original_coordinate %s.pdb %s.mbp
>analyze -c allpairs.ana
As for an example:
In the PDB format, these are the two values I'm interested in (moreso the B/temp-factor)
55 - 60 Real(6.2) Occupancy.
61 - 66 Real(6.2) Temperature factor (Default = 0.0).
As an example, I've included the pair extract from a random structure 1DQH.
For A(C 2) -- (G18)B, the B-factor averages would be:
A C2 All Nucleobase Average 28.6875
Base moeity average 24.095
Sugar moeity average 30.0375
Backbone moiety average 33.2125
B G18 All Nucleobase Average 22.9326087
Base moeity average 21.44
Sugar moeity average 23.7675
Backbone moiety average 25.21375
*This may not be correct, but I considered the backbone to be: P, OP1, OP2, O5', C5', C4', C3', O3'
Thanks so much!
Regards,
Isaac
17
General discussions (Q&As) / Re: B-Factor values from PDB in output files?
« on: February 13, 2013, 01:02:12 pm »
Hi,
Thanks for the reply!
In the context of .outp files, it seems like they would need their own subsection for crystal parameters. Occupancy seems appropriate.
If I had to do it manually, I was going to calculate the B-factor averages for individual base moieties:
Base A: Sum average, Backbone Avg, Sugar Avg, Base Avg.
Base B: Sum average, Backbone Avg, Sugar Avg, Base Avg.
**************
Crystal pair parameters
Strand I
base B-Factor Occupancy ...
1 A 55.0 1.0
.
.
.
Strand II
base B-Factor Occupancy ...
1 T 50.0 1.0
.
.
.
Thanks for the reply!
In the context of .outp files, it seems like they would need their own subsection for crystal parameters. Occupancy seems appropriate.
If I had to do it manually, I was going to calculate the B-factor averages for individual base moieties:
Base A: Sum average, Backbone Avg, Sugar Avg, Base Avg.
Base B: Sum average, Backbone Avg, Sugar Avg, Base Avg.
**************
Crystal pair parameters
Strand I
base B-Factor Occupancy ...
1 A 55.0 1.0
.
.
.
Strand II
base B-Factor Occupancy ...
1 T 50.0 1.0
.
.
.
18
General discussions (Q&As) / B-Factor values from PDB in output files?
« on: February 12, 2013, 05:30:59 pm »
Hi,
I've been looking through the documentation and can't seem to find any mention of this, but is there any way of getting the B-factor values for each base or base pair in the .outp files?
Thanks!
I've been looking through the documentation and can't seem to find any mention of this, but is there any way of getting the B-factor values for each base or base pair in the .outp files?
Thanks!
19
General discussions (Q&As) / Re: A way to regenerate experimental coordinates from the reference coordinates?
« on: July 09, 2012, 01:20:50 pm »
Oh man, you made my day.
Works perfectly for one structure so far, will let you know later after I've done it for many more.
Thank you so much!
Works perfectly for one structure so far, will let you know later after I've done it for many more.
Thank you so much!
20
General discussions (Q&As) / Re: A way to regenerate experimental coordinates from the reference coordinates?
« on: July 09, 2012, 12:40:33 pm »
Thanks so much for the prompt reply.
Pardon my poor phrasing. By parsing "hundreds of PDB's", I mean repeating the operation across hundreds of different PDB's to generate hundreds of different coordinate objects. I'm looking through essentially every base-pair (generated by your program) in the PDB for a specific marker. So for each NA PDB I'd run your program, look at the normal output, then (would like to) look at the exp. coordinates for each BP.
I've wrote the script you mentioned, but the best I can do is ~1k bp's per 5.48 seconds in Python. That'd be about 20-25 minutes for all the pairs I look at. C++ did 1k bp in about 0.17 sec with GCC optimization, but I'd like to stay away from compiled languages.
I'm definitely looking forward to the update. If you were able to include that in the update I'd just wait!
Thanks.
Pardon my poor phrasing. By parsing "hundreds of PDB's", I mean repeating the operation across hundreds of different PDB's to generate hundreds of different coordinate objects. I'm looking through essentially every base-pair (generated by your program) in the PDB for a specific marker. So for each NA PDB I'd run your program, look at the normal output, then (would like to) look at the exp. coordinates for each BP.
I've wrote the script you mentioned, but the best I can do is ~1k bp's per 5.48 seconds in Python. That'd be about 20-25 minutes for all the pairs I look at. C++ did 1k bp in about 0.17 sec with GCC optimization, but I'd like to stay away from compiled languages.
I'm definitely looking forward to the update. If you were able to include that in the update I'd just wait!
Thanks.
21
General discussions (Q&As) / Re: A way to regenerate experimental coordinates from the reference coordinates?
« on: July 09, 2012, 08:49:19 am »
Hi Xiang-Jun,
Thanks for the advice. I was hoping for an efficient way as Python can be rather slow when parsing hundreds or more PDB's, which is why I was wondering if there was a simple way to transform the local reference frame to the experimental coords as your program already parsed through the PDB's and organized the pairs so nicely. But I'll give it a shot to see if it doesn't cost too much wall-time.
Thanks
Thanks for the advice. I was hoping for an efficient way as Python can be rather slow when parsing hundreds or more PDB's, which is why I was wondering if there was a simple way to transform the local reference frame to the experimental coords as your program already parsed through the PDB's and organized the pairs so nicely. But I'll give it a shot to see if it doesn't cost too much wall-time.
Thanks
22
General discussions (Q&As) / A way to regenerate experimental coordinates from the reference coordinates?
« on: July 07, 2012, 05:28:47 pm »
Hi,
Love 3DNA and really appreciate its efficiency and speed. Have to admire some quality C coding!
I'm using a Python script that is tied to your program, but need the all-atom coordinates of every base-pair 3DNA finds. Your program generates a lovely allpairs.pdb file that contains all the information I need and would make life so much simpler, but unfortunately it is in a local reference frame.
I was wondering if there was a way to regenerate the coordinates of the native PDB from the generated allpairs.pdb file. Would this be a simple arithmatic operation, or a more complex matrix transformation that would require Lin. Alg. libraries? I've tried reading through the tech-details documentation, but am unclear as to how I could do this, if at all.
Thanks so much
Love 3DNA and really appreciate its efficiency and speed. Have to admire some quality C coding!
I'm using a Python script that is tied to your program, but need the all-atom coordinates of every base-pair 3DNA finds. Your program generates a lovely allpairs.pdb file that contains all the information I need and would make life so much simpler, but unfortunately it is in a local reference frame.
I was wondering if there was a way to regenerate the coordinates of the native PDB from the generated allpairs.pdb file. Would this be a simple arithmatic operation, or a more complex matrix transformation that would require Lin. Alg. libraries? I've tried reading through the tech-details documentation, but am unclear as to how I could do this, if at all.
Thanks so much
23
General discussions (Q&As) / Re: Extracting base-pair structural context from 3DNA output files of RNA
« on: May 11, 2012, 01:06:45 pm »
Hi esguerra,
Thanks so much. That's it.
Thanks so much. That's it.
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.
24
General discussions (Q&As) / Extracting base-pair structural context from 3DNA output files of RNA
« on: May 11, 2012, 12:34:39 pm »
First off, thanks for developing such an amazing tool.
To my question, I was reading the paper related to the BPS Database (doi: 10.1093/nar/gkn676) and in it they seem to imply they derive the structural context of base pairs (ie. Helical-Helical, Terminal helix-Helical stretch, etc) from some 3DNA output.
I've looked through the output files of a few simple RNA's I've run with your software but do not see this information anywhere. Am I missing something? Is this information not given by 3DNA directly? Or was it somehow indirectly derived by other output parameters by the authors of the BPS database?
Thanks!
To my question, I was reading the paper related to the BPS Database (doi: 10.1093/nar/gkn676) and in it they seem to imply they derive the structural context of base pairs (ie. Helical-Helical, Terminal helix-Helical stretch, etc) from some 3DNA output.
I've looked through the output files of a few simple RNA's I've run with your software but do not see this information anywhere. Am I missing something? Is this information not given by 3DNA directly? Or was it somehow indirectly derived by other output parameters by the authors of the BPS database?
Thanks!
Pages: [1]
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University