Dear all, I restart this topic because the problem was finally not solved...
Summary: - I am working on a structure with an unnatural ligand and I want to refine this ligand using coot. - Each time I try to import the .cif of my ligand produced by PRODRG web server or through CCP4/ProDrg, coot crashes with error message below (see quoted messages). - I sent my files to someone else and they are working on his computer (both are Mac and are using CCP4/Coot on same SBGRID server, with same files, and macOS was different). - I saw that my macOS was outdated (Starting SBGRID saying "- MacOS X versions 10.10 (Yosemite) and earlier are no longer officially supported"). - I did an update of my macOS to High Sierra (10.13.3). - I retried with same files, Coot crashed. - I went back to PRODRG server to generate a simple .cif (CH3-CH2-CH2-CH3). - I started Coot, opened the .cif file using "Import CIF dictionary...", Coot crashed. It seems that opening any .cif file on my computer causes Coot crash. Here are the terminal lines for Coot starting, .cif opening and crash; in which there is some WARNING I can't really understand completely (I'm not an unix power user). INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: > /programs/i386-mac/ccp4/7.0/ccp4-7.0/lib/data/monomers/ > INFO:: Reading coordinate file: > /programs/i386-mac/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb > PDB file > /programs/i386-mac/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb has > been read. > Spacegroup: P 1 > initalize graphics molecules...done. > (filter-fileselection-filenames-state) > (get-active-map-drag-flag) > (use-graphics-interface-state) > INFO:: coot.py imported > > ** (coot-bin:2710): WARNING **: Trying to register gtype > 'GMountMountFlags' as enum when in fact it is of type 'GFlags' > > ** (coot-bin:2710): WARNING **: Trying to register gtype > 'GDriveStartFlags' as enum when in fact it is of type 'GFlags' > > ** (coot-bin:2710): WARNING **: Trying to register gtype 'GSocketMsgFlags' > as enum when in fact it is of type 'GFlags' > INFO:: coot_python initialized > Running python script > /programs/i386-mac/ccp4/7.0/ccp4-7.0/lib/python2.7/site-packages/coot/coot_load_modules.py > Good Afternoon Username, Welcome to Coot version 0.8.9 > (set-display-intro-string "Good Afternoon Username, Welcome to Coot > version 0.8.9") > Coot Python Scripting GUI code found and loaded. > Coot Python Scripting GUI code found and loaded. > WARNING:: no directory "/programs/share/coot/pyextras" in > COOT_PYTHON_EXTRAS_DIR > /programs/share/coot/pyextras:/Users/Username/.coot-pyextras > WARNING:: no directory "/Users/Username/.coot-pyextras" in > COOT_PYTHON_EXTRAS_DIR > /programs/share/coot/pyextras:/Users/Username/.coot-pyextras > (use-graphics-interface-state) > (filter-fileselection-filenames-state) > (get-active-map-drag-flag) > (use-graphics-interface-state) > Coot Scheme Scripting GUI code found and loaded. > Good afternoon Username. Welcome to Coot 0.8.9. > (set-display-intro-string "Good afternoon Username. Welcome to Coot 0.8.9") > (set-display-lists-for-maps 0) > load /Users/Username/.coot-preferences/coot-preferences.scm > (set-filter-fileselection-filenames 0) > (unset-sticky-sort-by-date) > (set-colour-map-rotation-on-read-pdb 20.30) > (set-colour-map-rotation-on-read-pdb-c-only-flag 1) > (set-density-size 10.00) > (set-swap-difference-map-colours 0) > (set-active-map-drag-flag 1) > (set-idle-function-rotate-angle 1.00) > (filter-fileselection-filenames-state) > (get-active-map-drag-flag) > (use-graphics-interface-state) > (first-coords-imol) > > ** (coot-bin:2710): WARNING **: Widget not found: > cif_dictionary_file_selector_create_molecule_checkbutton > /programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288: 2710 > Segmentation fault: 11 $coot_bin "$@" > catching the crash log: > coot-exe: "/programs/i386-mac/ccp4/7.0/ccp4-7.0/libexec/coot-bin" > coot-version: > /programs/i386-mac/ccp4/7.0/ccp4-7.0/libexec/coot-bin > platform: > /usr/bin/uname > core: #f > No core file found. No debugging > Anybody has an idea to solve the problem? Thanks. Michel. 2018-03-06 16:03 GMT+01:00 M T <michel...@gmail.com>: > Last update... > > Everything works well with the same files and the same Coot version on an > other computer. The problem may come from the os of my computer which is > too old and has to be upgraded. > > Thank you for your help. > > 2018-03-06 9:20 GMT+01:00 M T <michel...@gmail.com>: > >> Dear all, >> >> I did something very simple... >> >> Starting from the pdb I obtained from PRODRG server (manual drawing, then >> transfer to PRODRG and download of the pdb from server), in CCP4 I used >> ProDrg to generate a new .cif and a new .pdb. >> After I used "View Job Results (ew style)" to open my new pdb in coot, I >> loaded the .mtz coming from the previous run of Refmac (in which I have a >> nice green blob corresponding to my ligand), I tried "Real Space Refine >> Zone" and ofc "Failed to find restraints for: DRG" since no .cif is loaded. >> I tried to import the .cif coming from CCP4/ProDrg, using "Import CIF >> dictionary..." and Coot crashed with this message: >> >> ** (coot-bin:5539): WARNING **: Widget not found: >>> cif_dictionary_file_selector_create_molecule_checkbutton >>> /programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288: 5539 >>> Segmentation fault: 11 $coot_bin "$@" >>> catching the crash log: >>> coot-exe: "/programs/i386-mac/ccp4/7.0/ccp4-7.0/libexec/coot-bin" >>> coot-version: >>> /programs/i386-mac/ccp4/7.0/ccp4-7.0/libexec/coot-bin >>> platform: >>> /usr/bin/uname >>> core: #f >>> No core file found. No debugging >>> >> >> At the loading of the molecule I have these messages: >> >> INFO:: Reading coordinate file: the path to my .pdb >>> PDB file my .pdb has been read. >>> No Spacegroup found for this PDB file >>> INFO:: Found 1 models >>> Model 1 had 0 links >>> WARNING:: No symmetry available for this molecule >>> WARNING:: No Symmetry for this model >>> in add_molecular_symmetry_matrices() made 0 biomt matrices >>> Molecule 0 read successfully >>> DEBUG:: there were 1 types with no dictionary >>> INFO:: comp-id: DRG is marked for non-autoloading - stopping now >>> (no-coot-tips) >>> (use-graphics-interface-state) >>> >> >> And nothing special at the reading of the .mtz file. >> >> The comparison of the naming in .pdb and .cif file reveals no evident >> difference (same molecule name DRG, and same atom names... I just compare >> the first 10/15 atom names). >> Is it a problem coming from my ligand, from Coot?... >> Could it be something related to that: >> >>> # WARNING: REFMAC5 uses columns 77-78 of PDB ATOM records to >>> # establish equivalence between model and topology. If >>> # you use O or other programmes that produce defective >>> # PDB files you must restore these columns, otherwise >>> # REFMAC5 will not recognise this topology. >>> >> Atom names are at different columns if the file is coming from >> CCP4/ProDrg or from Coot. Columns 77-78 in the file saved from Coot and >> columns 79-80 if the file is generated from CCP4/ProDrg. >> >> Thank you for your help. >> >> >> 2018-03-05 16:57 GMT+01:00 Eleanor Dodson <0000176a9d5ebad7-dmarc-reques >> t...@jiscmail.ac.uk>: >> >>> Herman is right - as long as refmac reads your generated DRG that is the >>> dictionary it will use.. >>> >>> My way of doing this sort of thing: >>> >>> Start with COOT with the DRG coordinates and ProDRG dictionary and try a >>> bit of real space refinement. >>> Coot should move the coodinates a bit and you should see something >>> happen. >>> >>> Then read out those new coordinates and run refmac. Again the coords >>> should move a bit, and at lest the B factors should change. If REFMAC >>> dooesnt like your naming it will report it.. >>> >>> Again if COOT accepted the dictionary the first time I cant see why it >>> wont read it again. are you sure you are finding the same cif file? >>> >>> You will have to read your own DRG into coot or otherwise it will find >>> something which is not appropriate for your problem.. >>> Eleeanor >>> >>> On 5 March 2018 at 13:36, <herman.schreu...@sanofi.com> wrote: >>> >>>> PS: If you have two different home-brewn ligands, you have to rename >>>> one of them (pdb and cif), otherwise the same dictionary will be applied to >>>> two different ligands. Also make sure your cif file is a dictionary and not >>>> just a coordinate file. >>>> >>>> HS >>>> >>>> >>>> >>>> *Von:* Schreuder, Herman /DE >>>> *Gesendet:* Montag, 5. März 2018 14:31 >>>> *An:* 'Colin Levy'; CCP4BB@JISCMAIL.AC.UK >>>> *Betreff:* AW: [ccp4bb] Small molecule not refined in coot. >>>> >>>> >>>> >>>> Hi Colin and Michel, >>>> >>>> >>>> >>>> In my experience, both refmac and coot will use the most recently >>>> read-in cif dictionary and there is no need to try to find an unique >>>> identifier for each new ligand one uses. The new dictionary overrides the >>>> old one. Finding a unique identifier for each new ligand would be a >>>> terrible and unnecessary hassle. >>>> >>>> >>>> >>>> What usually goes wrong is that the name of the residue in the pdb file >>>> does not match the name of the residue in the cif file. And the same holds >>>> for the atom names. I would check with an editor that the resdue and atom >>>> names of the pdb file do match the residue and atom names in the cif >>>> dictionary. >>>> >>>> >>>> >>>> Best, >>>> >>>> Herman >>>> >>>> >>>> >>>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK >>>> <CCP4BB@JISCMAIL.AC.UK>] *Im Auftrag von *Colin Levy >>>> *Gesendet:* Montag, 5. März 2018 13:38 >>>> *An:* CCP4BB@JISCMAIL.AC.UK >>>> *Betreff:* [EXTERNAL] Re: [ccp4bb] Small molecule not refined in coot. >>>> >>>> >>>> >>>> Hi Michel, >>>> >>>> >>>> >>>> If your ligand is designated as DRG in your pdb then refinement >>>> programs will anticipate that it is: >>>> >>>> >>>> Chemical Description >>>> >>>> *Name* >>>> >>>> 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE >>>> >>>> *Formula* >>>> >>>> C12 H11 N3 >>>> >>>> *Formal charge* >>>> >>>> 0 >>>> >>>> *Molecular weight* >>>> >>>> 197.236 g/mol >>>> >>>> *Component type* >>>> >>>> NON-POLYMER >>>> >>>> >>>> >>>> >>>> >>>> If this is not the case then you need to choose a unique identifier, >>>> this should then allow your cif library to be utilised appropriately during >>>> refinement. >>>> >>>> >>>> >>>> Colin >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Dr. Colin W. Levy >>>> >>>> MIB G016 >>>> >>>> Tel. 0161 275 5090 >>>> >>>> Mob.07786 197 554 >>>> c.l...@manchester.ac.uk >>>> >>>> >>>> >>>> Manchester Institute of Biotechnology | University of Manchester | >>>> 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN >>>> <https://maps.google.com/?q=131+Princess+Street+%7C+Manchester+%7C+M1+7DN&entry=gmail&source=g> >>>> >>>> >>>> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_MIB2006_-3Fref-3Daymt-5Fhomepage-5Fpanel&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=bKUGrH6wK5dQ2KLRw6oxFvnOjjWsZxfqbmZabgHnlnE&e=> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__plus.google.com_u_0_b_111834792186886067949_111834792186886067949_posts-3F-5Fga-3D1.142941878.209859079.1446729440&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=MxPD1QWp-GEhbvwGRdaEozWff1HvapFjYoa0O8j8ARY&e=> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_company_manchester-2Dinstitute-2Dof-2Dbiotechnology-3Ftrk-3Dbiz-2Dcompanies-2Dcym&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=NX4ub_6zOoHnKdhhIKKDNhy_ubtCXCpBDqtdRB6ChmM&e=> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_-3Flang-3Den-2Dgb-26lang-3Den-2Dgb&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=gNH6h2r1l3Fb1ho0UL9pWdjiU7yWfDS8tojGhnLoQE4&e=> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_channel_UCCBV8zDxk4L9yOEcujvSFNw&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=z2OpzMpJB9EYcL5yPECYcsocmhXktsEK-N_415fT35g&e=> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_channel_UCCBV8zDxk4L9yOEcujvSFNw&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=z2OpzMpJB9EYcL5yPECYcsocmhXktsEK-N_415fT35g&e=> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 5 Mar 2018, at 12:30, M T <michel...@gmail.com> wrote: >>>> >>>> >>>> >>>> Dear all, >>>> >>>> I am actually dealing with a structure containing an unnatural ligand. >>>> >>>> I generated the pdb file by drawing it on PRODRG server, I did a manual >>>> pre-fit in the map using coot and I manually merged the pdf file of my >>>> protein with the one of the ligand. >>>> >>>> After that I did few cycles of refinement using Refmac5, with my mtz, >>>> my merged pdb file and the cif library of the ligand as input files. >>>> >>>> First I saw that even if Refmac "completed succesfully" it didn't >>>> modify coordinates of the ligand, second I saw a warning about the "DRG" >>>> molecule in the log of Refmac (WARNING: duplicated name of monomer DRG Last >>>> entry will be used.), third in Coot I cannot use "Real Space Refine Zone" >>>> with the ligand and when I try to import the CIF dictionary produced by >>>> PRODRG (through the server or even the one generated through CCP4 ProDrg), >>>> it causes Coot crash (** (coot-bin:4467): WARNING **: Widget not found: >>>> cif_dictionary_file_selector_create_molecule_checkbutton >>>> /programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288: 4467 >>>> Segmentation fault: 11 $coot_bin "$@"). >>>> >>>> Clearly I am not a skilled user of all these programs, so I certainly >>>> did a/some mistake/s, but if someone can give me tips to be able to refine >>>> my ligand... Should I rename my DRG molecule, should I verify particular >>>> things, should I use other ways to generate the pdb and the library of my >>>> ligand? >>>> >>>> Thank you. >>>> >>>> >>>> >>>> P.S.: I am running CCP4 and coot using SBGRID on a Mac. >>>> >>>> Michel >>>> >>>> >>>> >>>> >>>> >>> >>> >> >
