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. >> >> I am still unsure the best way to move forward? >> >> >> >> ######################################################################## >> >> To unsubscribe from the COOT list, click the following link: >> >> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C01%7Clucrezia.catapano%40KCL.AC.UK%7C00c11d66a2174895349f08dbbde2bccb%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638312554015212820%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=l%2FLCOxYtGUdp122rDKOiqO2hHuDplXa6je8BhV%2Fq4Bc%3D&reserved=0 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> >> >> This message was issued to members of >> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCOOT&data=05%7C01%7Clucrezia.catapano%40KCL.AC.UK%7C00c11d66a2174895349f08dbbde2bccb%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638312554015212820%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NFHP3dlCIYTbb2yESbiNYngMmd%2Fm3uIjRfF6udVUMlE%3D&reserved=0 >> <http://www.jiscmail.ac.uk/COOT>, a mailing list hosted by >> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C01%7Clucrezia.catapano%40KCL.AC.UK%7C00c11d66a2174895349f08dbbde2bccb%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638312554015212820%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=T1LoniSJ07H1RMKT0b%2FBhiia97wuVxpX69%2B4W3HySF8%3D&reserved=0 >> <http://www.jiscmail.ac.uk/>, terms & conditions are available at >> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C01%7Clucrezia.catapano%40KCL.AC.UK%7C00c11d66a2174895349f08dbbde2bccb%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638312554015212820%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2xzjYZm7FzScC9Mv5FNTMYs9yjde6XAfOjl7WtCZ2hs%3D&reserved=0 >> <https://www.jiscmail.ac.uk/policyandsecurity/> >> <Screenshot 2023-09-29 at 10.46.21.png> >> >> >> >> ------------------------------ >> >> To unsubscribe from the COOT list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 >> > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list > hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > ------------------------------ > > End of COOT Digest - 29 Sep 2023 - Special issue (#2023-76) > *********************************************************** ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
