On 22/01/2022 22:10, Georg Mlynek wrote:

Dear Paul,

can you please tell me what the Acedrg Tables reference (I assume a table of curated stereochemistry values) and where I can find that table?

Where does coot save these cif files? (Not in CCP4-7\7.1\Lib\data\monomers\ as I always thought, before I tried now.)


Many thanks, br Georg.


Am 22.01.2022 um 22:51 schrieb Paul Emsley:


On 22/01/2022 21:47, Paul Emsley wrote:


On 22/01/2022 17:34, YUVARAJ I wrote:


I have solved a protein structure using anomalous signal using mercury(II)potassium Iodide(K2HgI4).

I wanted to submit the structure of the protein with mercury(II) potassium iodide to PDB.

I am facing problems while making the ligand (HGI4) . HGI4 is not available in the pdb.

Make Ligand in CCP4 is showing error

[...]

I have attached the screenshots for reference.



If it really is tetrahedral you could try the attached (TIM is already taken so you'll have to rename it  - or wwPDB will do it for you).

I desalted it of course. I also updated (hand-edited) the bond distances using the Acedrg Tables reference.

If successful, send us a picture of the post-refinement maps.


Sorry, I forgot to add:

Use File -> Import CIF dictionary

Tick the "Generate a Molecule" before clicking "Open"



The Acedrg tables are in $CCP4/share/acedrg/tables - they are tables, not cif files.

The particular file I used today was allMetalBonds.table.

Acedrg is not part of Coot, but it is part of CCP4.

Paul.




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