On 24/04/2020 15:16, Sebastian Falk wrote:
Dear CCP44bb community!
I am currently building and refining a structure and want to place
several iodines (IOD).
However, both COOT(0.8.9.2) does not refine IOD by real space
refinement after placing it as it misses the restraints.
Placing Chloride or Bromide works without problem.
I tried the following:
I tried to follow your working...
a) Extensions - Modelling - Add other solvent molecules. Typing the
comp.id <http://comp.id> IOD finds IODINE ION, but after placing it in
the density it does not refine.
I would have used "Place atom at pointer", FWIW - A bit less clicking -
and Coot knows that if you type "I" then it should make the comp_id be
"IOD".
b) I downloaded the IOD.CIF restraints and added them by: File -
Import CIF dictionary - does not work
:-( - by which I mean it should not be necessary to download IOD.cif -
and the Coot message has mislead you.
c) I checked the PDB file for the correct description of the comp.id
<http://comp.id> and heteroatom - but this is correct.
Indeed. Dictionary good, Coot bad.
d) I fetched a refined structure via PDB_redo that contains iodine
atoms and imported the CIF dictionary - but I get the same error message
Phenix does refine the IOD sites but coot and refmac dont recognise it.
For me, I get the warning about restraints, but Coot refines it anyway
(I tried Sphere refine, centred on the Iodine atom - and that was using
the Coot from CCP4 7.0). Or to put it another way, I got the first of
your dialogs that you sent, but not the second. Similarly for 0.9 - I
get the warning dialog, but the refinement happens OK anyway.
Coot presumes that if there are no bond restraints in the dictionary
that it just tried to read, then there was an error and tells you about
it. However, there is no error in the case for IOD. I will fix this
problem for 0.9.1.
Paul.
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