On 05/06/2025 13:30, Alejandro Buschiazzo wrote:
Dear cooters
:). Hi Alejandro.
I have a long list of residue side chains, whose planarity is to be
corrected.
I am at the end of refinement (against a 3.7Å res cryoEM map), so
already happy with many other validation indices (and especially, map
to model cross correlation), so would want to change the model as
little as possible.
My model is huge (many chains), which explains the long list of outliers.
Can I feed this properly into Coot 1.1.15, such that self restrains
are calculated (let’s say using a 5Å sphere for the whole molecule;
and that a pretty tight Gemann-McClure alpha parameter is set, like
0.01-0.03), and that then each of the listed residues gets
‘geometry-idealized’?
Yes.
I'd write a chapi script.
read in the map
read in the model
add local distance restraints for the whole model
set the weight
loop over the list of residues
residue_cid = residue_spec_to_residue_cid(residue_spec)
coot.refine_residues_using_atom_cid(imol, residue_cid, "SINGLE", 1000)
Given the many NCS relatives (many chains are identical in my
complex), doing this by hand is extremely slow, each time I say yes to
a correction, there’s a super long calculation (NCS matrix refinement)
going through ALL chains ….making this simple approach impracticable.
I don't like the sound of that. How can I reproduce this?
Paul.
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