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 +0000, 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 <[email protected]> on behalf of Eleanor Dodson > <[email protected]> > Sent: Thursday, January 27, 2022 6:25 AM > To: [email protected] <[email protected]> > 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 > <[email protected]<mailto:[email protected]>> 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 > <[email protected]<mailto:[email protected]>> 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 > <[email protected]<mailto:[email protected]>> > 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 > <[email protected]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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. > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > -- > > > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ######################################################################## > > 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/ ######################################################################## 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/
