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.
Kindly let me know How I could fix this ligand.
Thank you
Regards
Yuvara
On Tue, Jan 25, 2022 at 12:03 AM Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
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.
Dear Yuvara,
The molecules are in fact, in symmetry-related positions (which I
noticed after I sent the previous mail) - so three places that are
related by symmetry.
> I am getting the same output.
That cannot be true if you have deleted residues 180 and 181.
Indeed, you can look at the log files and see that those VDW outlier
warnings are no longer present. Now it is only crashing into a
symmetry-related water.
I think that model-building with symmetry turned on would help.
It is curious that refmac is scrunching the bond length down like that.
I now wonder if there is some nuclear-distance related discrepancy
between pyrogen and refmac. Try generating a map and difference map from
both 0 cycles and after 1 cycle. Try reducing the TIM occupancy to 0.6
or so (I imagine that that will make the difference map look better
(depending on the B-factors of course)).
Paul.
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