0176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> Sent: Thursday, January 27, 2022 6:25 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Make Ligand error
>
> YUVARAJI sent this email re HgI4 coordinates.
> The ligand problem has been solved and the map is beautiful, with very
Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, January 27, 2022 6:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Make Ligand error
YUVARAJI sent this email re HgI4 coordinates.
The ligand problem has been solved and the map is beautiful, with very
YUVARAJI sent this email re HgI4 coordinates.
The ligand problem has been solved and the map is beautiful, with very
sharp anomalous difference peaks showing I and HG.
It reveals a lot of substitution - five clusters to 175 residues and a lot
of alternate conformations. We tried many years ago to u
Respected Prof. Eleanor Dodson,
Thank you for your reply.
I have added Mercury(II) potassium iodide from (Heavy Atom screen Hg from
Hampton catlog no: HR2-446 )
https://hamptonresearch.com/uploads/support_materials/Heavy_Atom_UG.pdf
General observations about this Heavy atom: HgI3 can be formed
Dear Yuvara,
I have just read this..
Your first problem was that you had added the molecule at 3 symmetry
related positions, and once you corrected that the R factor dropped..
The negative density at the centre of your complex is odd.
Are you sure of its chemical composition?
On 25/01/2022 04:10, YUVARAJ I wrote:
Respected Prof. Paul
I added this ligand at three places, That why log file showed three
molecules,
I got multiple densities of the same ligand. For testing, I added it
at only one place and refined it.
It doesn't help, I am getting the same output.
Kin
On 24/01/2022 11:11, YUVARAJ I wrote:
Respected Prof. Paul,
Thank you for your kind reply, After refinement using refmac gives
output,
When I visualize in coot, the size of the molecule is small.
but when I do real space refinement with coot, It attains the original
size.
I have attached the
On 23/01/2022 09:56, YUVARAJ I wrote:
Respected Prof. Paul,
Thank you so much for your reply, I have followed your instructions,
while during refmac run,
It showed the error of "Error: New ligand has been encountered.
Stopping now"
when I gave the cif file as input in Additional geometry dicti
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,
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 Geo
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 probl
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 i
Dear Yuvaraj,
That is a lovely derivative, but the chemical species involved in that
derivatisation is not HgI4, nor the anion even (HgI4)2- , but is often the
anion (HgI3)- , with a nice symmetrical planar structure - see for instance
https://pubchem.ncbi.nlm.nih.gov/compound/Triiodo
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