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 output and refmac log file with this mail. kindly
let me know how I could fix this.
Many thanks in advance.
On Mon, Jan 24, 2022 at 12:39 PM Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
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
dictionary option in Refmac ,
It is giving the output (screenshot1) attached. Kindly give me
instructions or any link containing the steps, which I need to
follow.
As mentioned by Prof. Gerard, I have both tetrahedral ((HgI4)2-)
and trihedral (HgI3)-) electron densities.
Can you please send another cif file for (HgI3-) as well and set
of instructions, It will be very much helpful.
Thank you in advance.
Regards
Yuvaraj
On Sun, Jan 23, 2022 at 5:07 AM Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
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.
Hi Yuvaraj I,
Your log file does not contain a record of the command invocation
arguments unfortunately. But it does seem to me that you did not
specify LIBIN.
Paul.
Hi Yuvaraj I,
The log file says:
CGMAT cycle number = 1
**** VDW
outliers ****
VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be
monitored
A 179 TIM I1 . - A 180 TIM I4 . mod.= 0.001 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 179 TIM I1 . - A 181 TIM I1 . mod.= 0.001 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 1 -1 0 0 ncs 1 type = 10
A 179 TIM HG1 . - A 180 TIM HG1 . mod.= 0.000 id.= 2.200 dev=
-2.20 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 179 TIM HG1 . - A 181 TIM HG1 . mod.= 0.000 id.= 2.200 dev=
-2.20 sig.= 0.20 sym.= 1 -1 0 0 ncs 1 type = 10
A 179 TIM I2 . - A 180 TIM I3 . mod.= 0.000 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 179 TIM I2 . - A 181 TIM I2 . mod.= 0.001 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 1 -1 0 0 ncs 1 type = 10
A 179 TIM I3 . - A 180 TIM I2 . mod.= 0.001 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 179 TIM I3 . - A 181 TIM I3 . mod.= 0.001 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 1 -1 0 0 ncs 1 type = 10
A 179 TIM I4 . - A 180 TIM I1 . mod.= 0.000 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 179 TIM I4 . - A 181 TIM I4 . mod.= 0.000 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 1 -1 0 0 ncs 1 type = 10
A 180 TIM I1 . - A 181 TIM I4 . mod.= 0.000 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 180 TIM HG1 . - A 181 TIM HG1 . mod.= 0.000 id.= 2.200 dev=
-2.20 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 180 TIM I2 . - A 181 TIM I3 . mod.= 0.001 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 180 TIM I3 . - A 181 TIM I2 . mod.= 0.001 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
A 180 TIM I4 . - A 181 TIM I1 . mod.= 0.000 id.= 1.120 dev=
-1.12 sig.= 0.20 sym.= 5 -1 1 0 ncs 1 type = 10
So it seems to me that you have 3 ligands sitting on top of each other.
(The refmac interface in Coot runs read_refmac_log() which would have
brought that to your attention. You can invoke it using the Python
scripting interface if you wish: Calculate -> Scripting -> Python
read_refmac_log(0, "refmac.log") # or wherever it is)
Anyway, just delete A 180 and A 181 and thing will improve I suspect.
Paul.
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