Re: [ccp4bb] Make Ligand error

[Gerard Bricogne]

Dear Eleanor and Ron,

I remember seeing this derivative used to great effect by Alan Wonacott for
solving the structure of GAPDH from B. Stearothermophilus in 1973-75. The
data were collected on film by Jean-Claude Thierry on the first prototype of
the Arndt-Wonacott rotation camera and the processing was done by very
primitive software. As a PhD student (of David Blow) I had a chance to have
a hand in that phasing, first tweaking some parts of the PHARE program for
heavy-atom refinement and phasing, then grafting into it the calculation of
Hendrickson-Lattman coefficients for use in my phase combination program to
exploit the 222 NCS of these crystals.

Once I got the iterative NCS averaging plus phase combination to converge, I
remember putting those phases back into PHARE and re-refining the heavy-atom
parameters. Even with such rudimentary data collection hardware, there were
extremely clear (5-sigma, I think) peaks on the iodines in the anomalous
difference Fourier map in each copy of the protein. They were distributed at
the vertices of an equilateral triangle, with the Hg atom in the middle.

It gives a spectacular derivative when it binds. This was SIRAS phasing, but
it would be a real delight to do MAD phasing with, although probably quite
sensitive to radiation damage (however that can help the phasing too). 

With best wishes,

Gerard.

--
On Thu, Jan 27, 2022 at 06:35:08PM +, Ronald E. Stenkamp wrote:
> K2HgI4 worked for solving hemerythrin in 1975.  The various species of HgIx 
> in the solution found several binding sites.  Some were single Hg atoms 
> between cysteines and others were HgI bound elsewhere.  Ron Stenkamp
> 
> 
> From: CCP4 bulletin board  on behalf of 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 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 us this (pre-SAD phasing) 
> and again got too much substitution, not too little. Have other people used 
> it successfully? I would be interested to know..
> Eleanopr
> 
> On Tue, 25 Jan 2022 at 13:41, Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>> wrote:
> Thank you
> I can look at it and maybe be useful..
> HgI3c was a heavy atom we tried to use many years back for insulin!
> 
> Eleanor
> 
> On Tue, 25 Jan 2022 at 12:45, YUVARAJ I 
> mailto:yuvee...@gmail.com>> wrote:
> 
> 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 from K2HgI4 
> with the addition of excess KI.
> 
>  Using Anomalous signal obtained from this data, I have built the model using 
> CRANK2.
> 
> I will share the data and the pdb file with you.
> 
> It would be a great help, If you could help me in fitting this ligand.
> 
> Many Thanks
> 
> Yuvaraj
> 
> On Tue, Jan 25, 2022 at 5:18 PM Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
>  wrote:
> 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?
> And have you checked the peaks in the anomalous map.
> I can explain how to do that, or if you are allowed to send the data I can 
> show you what to expect.
> 
> Eleanor Dodson
> 
> 
> On Tue, 25 Jan 2022 at 04:41, Paul Emsley 
> mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
> 
> 
> 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 
> mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
> 
> 
> On 24/01/2022 11:11, YUVARAJ I wrote:
> Respected Prof. Paul,
> Thank you f

Re: [ccp4bb] Make Ligand error

[Ronald E. Stenkamp]

K2HgI4 worked for solving hemerythrin in 1975.  The various species of HgIx in 
the solution found several binding sites.  Some were single Hg atoms between 
cysteines and others were HgI bound elsewhere.  Ron Stenkamp


From: CCP4 bulletin board  on behalf of 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 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 us this (pre-SAD phasing) 
and again got too much substitution, not too little. Have other people used it 
successfully? I would be interested to know..
Eleanopr

On Tue, 25 Jan 2022 at 13:41, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Thank you
I can look at it and maybe be useful..
HgI3c was a heavy atom we tried to use many years back for insulin!

Eleanor

On Tue, 25 Jan 2022 at 12:45, YUVARAJ I 
mailto:yuvee...@gmail.com>> wrote:

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 from K2HgI4 with 
the addition of excess KI.

 Using Anomalous signal obtained from this data, I have built the model using 
CRANK2.

I will share the data and the pdb file with you.

It would be a great help, If you could help me in fitting this ligand.

Many Thanks

Yuvaraj

On Tue, Jan 25, 2022 at 5:18 PM Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
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?
And have you checked the peaks in the anomalous map.
I can explain how to do that, or if you are allowed to send the data I can show 
you what to expect.

Eleanor Dodson


On Tue, 25 Jan 2022 at 04:41, Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:


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 
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 
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 
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 

Re: [ccp4bb] Make Ligand error

[Eleanor Dodson]

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 us this (pre-SAD
phasing) and again got too much substitution, not too little. Have other
people used it successfully? I would be interested to know..
Eleanopr

On Tue, 25 Jan 2022 at 13:41, Eleanor Dodson 
wrote:

> Thank you
> I can look at it and maybe be useful..
> HgI3c was a heavy atom we tried to use many years back for insulin!
>
> Eleanor
>
> On Tue, 25 Jan 2022 at 12:45, YUVARAJ I  wrote:
>
>> 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 from
>> K2HgI4 with the addition of excess KI.
>>
>>  Using Anomalous signal obtained from this data, I have built the model
>> using CRANK2.
>>
>> I will share the data and the pdb file with you.
>>
>> It would be a great help, If you could help me in fitting this ligand.
>>
>> Many Thanks
>> Yuvaraj
>>
>> On Tue, Jan 25, 2022 at 5:18 PM Eleanor Dodson <
>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> 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?
>>> And have you checked the peaks in the anomalous map.
>>> I can explain how to do that, or if you are allowed to send the data I
>>> can show you what to expect.
>>>
>>> Eleanor Dodson
>>>
>>>
>>> On Tue, 25 Jan 2022 at 04:41, Paul Emsley 
>>> wrote:
>>>

 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 
 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> 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> 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 

Re: [ccp4bb] Make Ligand error

[YUVARAJ I]

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 from K2HgI4
with the addition of excess KI.

 Using Anomalous signal obtained from this data, I have built the model
using CRANK2.

I will share the data and the pdb file with you.

It would be a great help, If you could help me in fitting this ligand.

Many Thanks
Yuvaraj

On Tue, Jan 25, 2022 at 5:18 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> 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?
> And have you checked the peaks in the anomalous map.
> I can explain how to do that, or if you are allowed to send the data I can
> show you what to expect.
>
> Eleanor Dodson
>
>
> On Tue, 25 Jan 2022 at 04:41, Paul Emsley 
> wrote:
>
>>
>> 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 
>> 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 
>>> 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 
 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 

Re: [ccp4bb] Make Ligand error

[Eleanor Dodson]

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?
And have you checked the peaks in the anomalous map.
I can explain how to do that, or if you are allowed to send the data I can
show you what to expect.

Eleanor Dodson


On Tue, 25 Jan 2022 at 04:41, Paul Emsley  wrote:

>
> 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 
> 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 
>> 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 
>>> 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
>>
>> A179 TIM I1  . - A180 TIM I4  . mod.= 0.001 id.= 1.120 dev= -1.12
>> sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
>> A179 TIM I1  . - A181 TIM I1  . mod.= 0.001 id.= 1.120 dev= -1.12
>> sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
>> A179 TIM HG1 . - A180 TIM HG1 . mod.= 0.000 id.= 2.200 dev= -2.20
>> sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
>> 

Re: [ccp4bb] Make Ligand error

[Paul Emsley]

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 
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
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
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  

Re: [ccp4bb] Make Ligand error

[Paul Emsley]

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 
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
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 

Re: [ccp4bb] Make Ligand error

[Paul Emsley]

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 > 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.







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Re: [ccp4bb] Make Ligand error

[Paul Emsley]

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.






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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Re: [ccp4bb] Make Ligand error

[Georg Mlynek]

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"





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 







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Re: [ccp4bb] Make Ligand error

[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"





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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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Re: [ccp4bb] Make Ligand error

[Paul Emsley]

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.

Paul.





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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TIM-pyrogen.cif
Description: CIF chemical test

Re: [ccp4bb] Make Ligand error

[Gerard Bricogne]

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/Triiodomercurate_1

The Molfile and SDF files at 

   https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51567

contain coordinates for the Mercury and Iodine atoms that should enable you
to create a dictionary for it. Or perhaps someone else can direct you to a
a ready-made refinement dictionary - I couldn't find one.


 With best wishes,

  Gerard.

--
On Sat, Jan 22, 2022 at 11:04:27PM +0530, YUVARAJ I wrote:
> Respected Professors,
> 
> 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
> 
> " The input ligands/molecules contains metal or other heavier atoms
> 
> Acedrg currently deals with ligands/molecules with following elements only
> 
> C, N, O, S, P, B, F, Cl, Br, I, H"
> 
> I tried to make cif file from other softwares, given as input in coot, It
> is also showing errors,  dictionary no restraints were found.
> 
> For generating cif dictionary, I used prodrg server
> 
> It is showing error
> 
> "PRODRG> Found unsupported atom HG in Molfile.
> 
>  ERRDRG> Currently only N, C, O, S, P, Cl, Br, F, I are supported. "
> 
> 
> If I fix each atom seperately such as Hg and Iodine separately, It is
> having clashes with other atoms during validation,
> 
> kindly let me know how I can fix this HGI4 ?
> 
> I have attached the screenshots for reference.
> 
> -- 
> 
> Regards
> Yuvaraj
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/



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