Topics

1

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.

2

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

3

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.

   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]

4

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

5

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!

6

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

7

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!