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/
