> Sorry if this is not the place to post this but,
> how do I interpret the pdb files? Assignement 4 asks ...
This is exactly the right thing to do Stephen!, except I suggest
we transfer the discussion to VSNS-PPS-BACKBONE as this relates directly
to the course subject material. I'm not going to explain in detail - I'll
leave that to another course member since everyone learns more that way.
Some comments:
- There *is* a precise specification for all the records in a PDB
file. So find the manual under the PDB home page - it's something worth
having a look at as there are many things in PDB files which most people
don't use because they don't realise what they are for.
- Think about how you might describe a SHEET. What needs to be said?
Have a look on RasMol as see what sense you can make of the residues that
'go backwards'. What are the 'O' and 'N' doing? Why is there a '-1'?
- Data files aren't always easy to read by eye and there are
parts of this file (like many others) that won't make sense without the
manual (although you can sometimes make inspired guesses). For this
reason the modern trend is either towards data files with more
descriptive keywords in ('semantics') or to provide special tools to read
and write them.
We shan't spend a lot more time in the course looking at the
details of the PDB file after this, but since it is so central to
protein structure it's important to know that there *may* be a lot of useful
stuff there.
I'd welcome other comments and help from course members.
P.
Peter Murray-Rust, Glaxo Research & Dev. (pmr1716@ggr.co.uk); (BioMOO: PeterMR)
Birkbeck College, ubcg09q@cryst.bbk.ac.uk, CBMT/Daresbury mbglx@seqnet.dl.ac.uk
http://www.cryst.bbk.ac.uk/PPS/index.html, http://www.dl.ac.uk/CBMT/HOME.html