On 01/02/2021 13:23, leo john wrote:
I am sure this issue might have addressed before,
Correct.
but somehow I am not able to find it.
That's because email is a terrible system for archiving structural biology information. An that goes doubly
so for the Jiscmail archive.
We should use something better.
After refinement when I open the structure in coot and draw the unit cell, I find that the modeled molecule
is not centered in the cell (unitcell.png)
Please suggest me a way by which I can get the molecule centered.
Centre (using middle mouse click) on an atom in the symmetry-related molecule that you would actually like
to be the "main" molecule, then Calculate -> Modelling -> Symm Shift Reference Chain Here.
I have a Bromo-phenylalanine in the sequence that I have modeled, but I get the red and green density around
Br atom (brphe.png). What can be the possible reason and how can I get rid of it.
Tha looks right out of Dale's "Introduction to Maps" presentation. It's anisotropy. Thing about what you'd
get if you subtract a gaussian sphere from a gaussian ellipsoid. You can either model it with anisotropic
B-factor refinement (perhaps just that atom) or maybe split the residue by adding an alt conf.
Paul.
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