From: Michael Weber <weberm@st...> - 2007-09-09 12:37:34
maybe this has been asked before, but I could not find any hints
concerning this issue in the PyMOL wiki, so here it goes:
I am trying to build a computer model for a yet structurally
uncharacterized non-coding bacterial RNA molecule. To do this, I have
already constructed a consensus secondary structure model based on a
multiple sequence alignment and in-depth phylogenetic covariance
analyses that also includes some experimental secondary structure
mapping data. I am now trying to find structurally characterized RNA
sequence fragments in the PDB database that are identical to parts of my
sequence in order to compare whether they are part of a similar
secondary structure element as I find in my molecule. If so, I want to
use these regions as a basis for structure model generation. This
procedure seems to require excessive screening of many PDB files.
Now my question: Is it possible to search for a primary sequence within
PyMOL? Let's say, I have opened a ribosome PDB file and I just want to
find the RNA sequence fragment UGUUCGC in chain A which according to
BLASTN (previously run against PDB using that sequence) is definetely
part of the structure. Is there a convenient method to do that?
Moreover, is it possible to automatically search and retrieve all PDB
files from the PDB database that contain a specified sequence segment?
Could a future version of PyMOL please also include nucleic acid
building blocks in the builder module?
Generally speaking, I am quite disappointed how few nucleic acid-related
functions are available in current bioinformatic software products and
this in the light that even last year's nobel prize has been given for
RNA-related research. It might be a bit hard to perceive for the protein
guys among us (and I was a "pure proteomics guy", too - some years ago -
;-), but I expect the major future breakthroughs in research in the
field of RNA rather than proteins. Therefore, I would be happy if one of
my favourite programs, PyMOL, would be further developed in a way that
takes this expectation into account, especially since our work group has
just decided to support this project financially, too.
I also wonder whether there are any plans to extend the capabilities of
PyMOL beyond a "structure viewer" program?
Best regards & thanks for your help,