On 26/09/2018 04:02, Yangqi Gu wrote:
I have a question regarding to model building. I am trying to trace my protein
backbones manually. I have a helix EM map,
Do you mean "helical" - something with alpha helices in? Then I'd use "Place Helix
Here"
Or a helical reconstruction? There is nothing special about this - with the exception of the application of
helical symmetry molecules. You will need to know your rotation/transformation matrix (easier if the helix
is along z). Most people here though don't do that - they construct 5 "real" molecules and do their
model-building/correction on the middle ("C") chain and then apply C model to A,B,D,E before refinement.
but I only wanted to trace my monomer backbones.
In today's Coot, I'd use the Baton Builder - as long as you can see hints of side-chains, you can build ~200
amino acid backbone in a few minutes (with some practice).
You might like to consider buccaneer, an interface to which is available in
CCPEM.
I am wondering if there is anyway to cut out the monomer?
Yes there is - File -> Export Map Fragment, I am not sure that that's what you
need though.
Also,could anyone explain to me how Baton modes decide the starting point?
This is not intuitive it seems. The CA atoms are added to the tip of the baton, not the base. The base
starts at the centre of the screen, so if you know where the first CA atom should be, you need to start with
the screen centre ~3.7A away from that. You can use the cross-hairs to show you where.
Paul.
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