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 <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 <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 < >> 0000176a9d5ebad7-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 <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 <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> 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 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 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/
