Hi Oliver! Yes that is what I see in my foot when I fetch from different sources
I started looking at the lines of the PDB too to see if there are any striking differences. -- Kelvin Lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin....@epfl.ch<mailto:kelvin....@epfl.ch> Phone: +41 21 69 34494 On 29 Sep 2023, at 14:36, Oliver Clarke <olibcla...@gmail.com> wrote: Whoops sorry - corrected link: https://www.dropbox.com/scl/fi/t113o9lgprboqycz21ryc/mdo_7tqr.mov?rlkey=y8154e0t5gc6y6odnfhplo9qf&dl=0 On Sep 29, 2023, at 8:31 AM, Oliver Clarke <olibcla...@gmail.com> wrote: For me, MDO in 7tqr blows up if I use the model/map from “Fetch PDB & Map using EDS”, using Coot 0.9.8.91 EL (CCP4): https://www.dropbox.com/scl/fi/yw4nkiz9zmpms7gx3ie1h/7tqr_mdo.mov?rlkey=rtpo3vcl0jy7tha1qd8t82goz&dl=0 But interestingly, if I use the PDB and map from PDB-REDO, it refines just fine! Maybe a hint there? Cheers Oli ---------------------------------------------------------------------- Date: Fri, 29 Sep 2023 12:59:25 +0100 From: Eleanor Dodson <eleanor.dod...@york.ac.uk> Subject: Re: MDO Unnatural modified Amino acid Hmm - 7tqr downloaded from pdb now just works for me? sphere refine around the MDO is all OK. From log file.. Running python script /Applications/ccp4-8.0/coot_py2/lib/python2.7/site-packages/coot/coot_load_modules.py Good Morning Eleanor, Welcome to Coot version 0.9.8.91 MDO labelled no polymer but COOT must recognise it is a peptide.. From COOT log INFO:: using standard CCP4 Refmac dictionary to search for "MDO" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/m/MDO.cif ..... Made 485 link trans-peptide restraints DEBUG:: make_other_types_of_link() "pept-MDO" for [spec: model 1 "A" 140 "" " N " ""] [spec: model 1 "A" 141 "" " N " ""] detected DEBUG:: make_other_types_of_link(): now making a link restraint [spec: 1 "A" 140 ""] [spec: 1 "A" 141 ""] with type pept-MDO and order switch 0 DEBUG:: make_other_types_of_link() "MDO-pept" for [spec: model 1 "A" 141 "" " CA3" ""] [spec: model 1 "A" 144 "" " N " ""] detected DEBUG:: make_other_types_of_link(): now making a link restraint [spec: 1 "A" 141 ""] [spec: 1 "A" 144 ""] with type MDO-pept and order switch 0 On Fri, 29 Sept 2023 at 12:24, Kelvin Lau < 00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote: Dear Lucrezia Thanks for your reply! 1) I just tried this on 0.9.8.91 EL and up until sphere refine, everything works well. However the refinement does not refine.. As you can see from the screenshots the MDO fits perfectly before refinement, but even with the auto detected links, it fails. [image: PastedGraphic-2.png][image: PastedGraphic-1.png] 2) I also attempted to fetch 7tqr via EDS and PDB-Redo to see if there are differences within the PDBs and the links. What I found is that the EDS version of the PDB, if I just do not change anything and do a sphere refine, the MDO does not refine. However, the PDB fetched by PDB-REDO, I can now directly refine this structure. Looking into the PDB I dont really see anything that is distinct in between the two. Dont know if this is related or not Best Kelvin -- Kelvin Lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin....@epfl.ch Phone (office) : +41 21 69 30267 Phone (everywhere else) : +41 21 69 34494 On 29 Sep 2023, at 11:47, Lucrezia Catapano <lucrezia.catap...@kcl.ac.uk> wrote: Hi Kelvin, I tried the following on 7tqr, and it seems to work. I am using coot 0.9.8.92 (CCP4): Get monomer MDO merge MDO in the model and fit into the density MDO now has number 617, this needs to be changed to 141. Edit renumber residue: select the model, and then ‘Start Residue’ 617, ‘End Residue’ 617 and ‘Apply Offset’: -476. See screenshot When you click apply you can see that the link is formed, however the OXT is not deleted (Bug!). Delete OXT and H2 and do sphere refinement. Lucrezia *From: *Mailing list for users of COOT Crystallographic Software < COOT@JISCMAIL.AC.UK> on behalf of Kelvin Lau < 00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> *Date: *Monday, 25 September 2023 at 17:16 *To: *COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK> *Subject: *Re: MDO Unnatural modified Amino acid [You don't often get email from 00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Dear all Thank you for looking into this. @Keitaro: I forgot to say I am on 0.9.8.91 EL (ccp4) build. If I just refine the MDO (A/141) or residues 140-141 together, both ways, the ligand moves out of the density and the stats become all red. However, I do see that the links are there. Today I have tried the following just to test in the 7tqr PDB : -Fetch MDO residue from within COOT (success) -Delete the OXT and H2 atoms manually (success) -refine into density (success) -merge into chain A (success) Option A: rename residue (in 7tqr) to 142. The Nterminal residue is 140 and Cterminal is 144. I observe that COOT thinks there must be some sort of peptide link as it tries to link into the mainchain. Option B: keep residue inserted as 6XX. Manually "link residues" within COOT at the C and N-terminus to N-140 and C-144. -For both Option A or B - real space refinement leads to a disaster of atoms everywhere. 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