Messages

1

RNA structures (DSSR) / 1ffk missing nucleotides?

« on: May 21, 2015, 08:19:56 pm »

Hi Xiang-Jun,

I am comparing the structures output by DSSR to those in FRABASE.  For the structure 1ffk, the DSSR output contains something like:

U&A
(&)

The structure in FRABASE for this same regions shows:

UCUAA
(---)

http://rnafrabase.cs.put.poznan.pl/?act=pdbdetails&id=1FFK

Note the CUA that is missing from DSSR's output.  It appears that DSSR is dropping the nucleotides between chains.  Therefore the whole chain output is incomplete if ampersands (&) are removed.

Is there a way to have DSSR output the whole sequence with missing nucleotides separated by "-" characters, as in the output from FRABASE?

Thanks,
Erik

2

RNA structures (DSSR) / Re: 1h1k secondary structure

« on: May 21, 2015, 11:59:23 am »

Hi Xiang-Jun,

Thank you for the thorough reply.

One related question:  When specifying --nest, is this equivalent to replacing all {}, <>, etc. with "." in the DBN?  Or does --nest do something more complicated?

Thanks again,
Erik

3

RNA structures (DSSR) / 1h1k secondary structure

« on: May 21, 2015, 07:36:56 am »

I am trying to understand the secondary structure for PDB 1h1k [whole chain].  This is a series of A's followed by U's.  When I compute the structure with DSSR, it looks something like:

((([[[{{{)))]]]}}}

I think that this indicates there is a pseudo-knot.

If the option --nest is added, the structure looks something like:

(((....)))....

I expected the structure in both cases to look something like:

(((((())))))

I suspect that this has something to do with the fact that the structure is split into multiple chains.

The actual outputs are attached.  I am using DSSR v1.2.6-2015mar28.

I would appreciate if the structures could be explained, so that I can better understand the outputs in this case.

Thanks, Erik