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.
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
