Re: [COOT] MDO Unnatural modified Amino acid
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 wrote: Whoops sorry - corrected link: https://www.dropbox.com/scl/fi/t113o9lgprboqycz21ryc/mdo_7tqr.mov?rlkey=y8154e0t5gc6y6odnfhplo9qf=0 On Sep 29, 2023, at 8:31 AM, Oliver Clarke 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=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 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 < 5aaf8435dbef-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 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 < 5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> *Date: *Monday, 25 September 2023 at 17:16 *To: *COOT@JISCMAIL.AC.UK *Subject: *Re: MDO Unnatural modified Amino acid [You don't often get email from 5aaf8435dbef-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. H
Re: [COOT] MDO Unnatural modified Amino acid
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://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
Re: [COOT] MDO Unnatural modified Amino acid
Hi Eleanor
Thanks for catching that..
I was under the impression that when I am fetching the monomer, MDO, it was
defined as a peptide, not a non polymer … at least that’s what is listed here:
https://www.rcsb.org/ligand/MDO
I guess I have to go about as Paul suggested as changing it to “peptide”
Is an alternative using the PDB MDO cif file as the restraint as it is properly
defined and replacing the original definition?
--
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 21 Sep 2023, at 22:56, Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
And in fact it doesnt..
data_comp_list
loop_
_chem_comp.id<http://chem_comp.id>
_chem_comp.three_letter_code
_chem_comp.name<http://chem_comp.name>
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
MDO MDO
"{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid" NON-POLYMER 24 14 .
#
On Thu, 21 Sept 2023 at 21:53, Eleanor Dodson
mailto:eleanor.dod...@york.ac.uk>> wrote:
Check the dictionary has labelled it as peptide
like ALA
data_comp_list
loop_
_chem_comp.id<http://chem_comp.id>
_chem_comp.three_letter_code
_chem_comp.name<http://chem_comp.name>
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
ALA ALA ALANINE peptide 13 6 .
On Thu, 21 Sept 2023 at 18:58, Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 21/09/2023 18:05, Kelvin Lau wrote:
> Dear all
>
> I am having trouble with an unnatural ligand/amino acid.
>
> I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO
> residue that replaces three residues in a series G-A-S-G-D to become G-MDO-D.
> MDO is in the Coot library.
>
> I have been very used to replacing cysteines with CME with Modelling>Replace
> residue. It works great, removes the OXT and all the other atoms, can use
> real space refine directly.
>
> For this MDO residue I find that it correctly fetches from the dictionary,
> however, I cannot refine it. Whenever I click on an atom and drag it just
> blows up or the atom gets stuck.
>
> I have now opened up 6Q6H and 7TQR and tried to just refine the built in MDO
> in those PDB, same thing happens.
>
> Does anyone have any ideas of what might be going on? Also in general for
> modified residues/unnaturals.
If you tell Coot that the group is a non-polymer it will believe you.
Use the Restraints editor to change the group to "peptide" (not tested).
Paul.
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[COOT] MDO Unnatural modified Amino acid
Dear all I am having trouble with an unnatural ligand/amino acid. I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO residue that replaces three residues in a series G-A-S-G-D to become G-MDO-D. MDO is in the Coot library. I have been very used to replacing cysteines with CME with Modelling>Replace residue. It works great, removes the OXT and all the other atoms, can use real space refine directly. For this MDO residue I find that it correctly fetches from the dictionary, however, I cannot refine it. Whenever I click on an atom and drag it just blows up or the atom gets stuck. I have now opened up 6Q6H and 7TQR and tried to just refine the built in MDO in those PDB, same thing happens. Does anyone have any ideas of what might be going on? Also in general for modified residues/unnaturals. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
Re: [COOT] coot on MacOS
When Xquartz is installed it should be in the applications folder. Have you tried to reinstall it? It should open an installer gui and proceed normally. -- 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 31 Aug 2023, at 22:52, Andrea Smith wrote: P.S. Found this in the log file from Cloud: dyld: Library not loaded: /usr/X11/lib/libpixman-1.0.dylib Referenced from: /Applications/ccp4-8.0/lib/libcairo.2.dylib Reason: Incompatible library version: libcairo.2.dylib requires version 35.0.0 or later, but libpixman-1.0.dylib provides version 0.0.0 /Applications/ccp4-8.0/coot_py2/bin/coot: line 272: 3147 Abort trap: 6 $coot_bin "$@" ERROR: In procedure dynamic-link: ERROR: file: "libguilegtk-2.0", message: "file not found" *** error running coot: Error in command.call Return code: 34304 On Thursday, August 31, 2023 22:18 CEST, Andrea Smith wrote: Dear all, I have macOS Big Sur version 11.6.8 (first time Mac user) and I wanted to get CCP4. So I went to CCP4 download pages, there I read I need XQuartz, so I downloaded XQuartz 2.8.3. Installed. Then I downloaded the CCP4 Package Manager. Installed. Tried to run CCP4 Cloud. All good until I wanted to open Coot which failed on the Cloud. So I tried to open Coot directly from Applications, but Coot doesn't open. The XQuartz is not in the Applications (?). What am I doing wrong? How do I find out where is the problem? Help will be appreciated. Thank you, best, Andrea To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
[COOT] 0.9.8.6 Carbohydrate linking issue still
Dear Paul I looked back the forum and similar to Taka's issue in 0.9.8.4 I am also experience it with both Coot 0.9.8.6 EL (ccp4 build) and 0.9.8.5 (ccpEM) build. MacOS 12.6.1 It seems very similar to Taka's issue where if I add an NAG using the Carbohydrate module, I get my NAG, but no link. I only recently updated to 0.9.8.6 (dont remember what version I was using before), but there were no problems then. Attaching the terminal output below. Looks like the NAG-ASN links and files are missing?? INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/n/NAG.cif INFO:: using standard CCP4 Refmac dictionary to search for "BMA" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/b/BMA.cif INFO:: using standard CCP4 Refmac dictionary to search for "MAN" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/m/MAN.cif INFO:: using standard CCP4 Refmac dictionary to search for "GAL" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GAL.cif INFO:: using standard CCP4 Refmac dictionary to search for "GLC" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GLC.cif INFO:: using standard CCP4 Refmac dictionary to search for "FUC" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/f/FUC.cif INFO:: using standard CCP4 Refmac dictionary to search for "XYP" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/x/XYP.cif INFO:: using standard CCP4 Refmac dictionary to search for "BGC" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/b/BGC.cif . checking for /Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab ..that failed - trying /Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /Applications/ccp4-8.0/coot_py2/share/coot/NAG-decorations.tab WARNING:: Link not found in dictionary WARNING:: Neither index2 15 nor index3 14 has forward atoms! INFO:: replace_coords: 22 atoms updated. model file does not exist "/Users/jenkins/workspace/CCP4/coot-py2-osx-clang/devtools/install/share/coot/data/cho-models/model-level-1-NAG-NAG-ASN-ASN.tab" - in create_mmdbmanager_from_res_vector() alt_conf is "" - in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 38 atoms debug:: on creation last_restraints is 0x7fb326b64200 INFO:: from_res_vec() created 108 monomer restraints created 35 bond restraints created 43 angle restraints created 5 plane restraints created 8 chiral vol restraints created 0 improper dihedral restraints created 17 torsion restraints Made 2 link bond restraints Made 6 link angle restraints Made 4 link plane restraints Made 0 link trans-peptide restraints link type "NAG-ASN" not found in dictionary!! To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
