On 7/1/24 12:24, Noha Elhosseiny wrote:
Thanks Paul,
I replied below in a different color
On Mon, Jul 1, 2024 at 2:17 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:
On 01/07/2024 11:59, Noha Elhosseiny wrote:
>
>
> --
>
>
>
> I am new to coot and structural analysis in general. I am trying
to do
> model building for a symmetric protein consisting of 15 identical
> chains, using the density map from cryoEM analysis. I made an
initial
> model by first fitting one chain (chain A- roughly) in Chimera,
copied
> this chain to make the 15-mer, and then moved to coot for
refinement
> and improving the fitting. I noticed that there is a slight
shift from
> the best fit of the chain I fitted and then copied (chain A) in the
> other chains in the density map. To cut it short chain A is
perfect,
> but chains B-O gradually shift very slightly from the ideal fit,
> probably as a result of the copying process. Now I am not sure
what to
> do. I can try to work on each chain individually to fall into the
> density like I did with chain A, but it seems counterintuitive
to do
> this 14 times when I already have a perfect chain.... I considered
> doing LSQ superpose of chain A on each of the other chains, but
given
> they are already shifted...I think this will not solve the
problem. I
> also think I can try to do "refine chain" or "jiggle fit", but I
think
> this will make it worse not better as the chains are very slightly
> shifted.....
>
> Any suggestions on how to proceed?
>
Presumably you have the transposition matrices from your cryo-EM
processing. I imagine that it might even be proper symmetry. You
can use
that. What molecular symmetry do you have?
I suppose I have...but I do not know how to get these matrices or
where to look for them....I am using CryoSPARC. I can look into where
to get them. I have a C15 symmetry and I am 90% sure it is correct as
the protein is not new but the species is and there are sequence
differences.....
One generally modifies only one copy. When refining, one might make a
molecule of 5 chains (to model the interaction between chains) and then
modify only the middle (C) chain.
You only need do the full symmetry expansion for deposition and making
figures.
Attached is a script to do what you want (as far as I can tell) - you
will need to change the imol file and the centre to be appropriate for
your molecule.
Paul.
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import math
imol = read_pdb('my-chain.pdb')
# the should be the centre of your map, we presume that the centre of
# the map is the centre of the (model) molecule:
centre = [467.04/2, 467.04/2, 467.04/2]
n_copies = 15
imol_copies = []
for c in range(1, n_copies):
theta = c * 2.0 * math.pi / n_copies
ct = math.cos(theta)
st = math.sin(theta)
imol_copy = copy_molecule(imol)
imol_copies.append(imol_copy)
translate_molecule_by(imol_copy, -centre[0], -centre[1], 0)
transform_molecule_by(imol_copy, ct, -st, 0, st, ct, 0, 0, 0, 1, 0, 0, 0)
translate_molecule_by(imol_copy, centre[0], centre[1], 0)
merge_molecules(imol_copies, imol)
write_pdb_file(imol, "molecule-with-all-the-symm.pdb")
