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 <[email protected]> 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 <[email protected]>
> 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 <[email protected]>
>> 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 <[email protected]>
>>> 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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