Re: [COOT] replace residue Cd not active
Ahhh...it did replace two residues, but I didn't see the change in the sequence viewer, I think I need to merge maps 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] replace residue Cd not active
I found the simple mutate on the right vertical and attempted to mutate to Cytosine and got the following response setup-mutate 1) (0) " C1'"/1/chainid="C"/1401/DC, occ: 1 with B-factor: 53.31 element: " C" at (-1.533,-49.588,103.117) : 0.131962 (setup-mutate 0) Pending Picks Cleared INFO:: backup file name coot-backup/_home_paul_ccp4_pdbs_PIC_c3DNA_1d3u.cif-coot-0.pdb_Mon_Dec_12_11:10:11_2022_modification_2.pdb.gz INFO:: 6 matched atoms had: mean devi: 9.6702e-15 rms devi: 1.16229e-14 max devi: 1.42542e-14 min devi: 2.22045e-16 (update-go-to-atom-window-on-changed-mol 0) 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] replace residue Cd not active
I am not seeing "Simple Mutate". I apologize I am learning. I have collumns File, Edit, Draw, Measures, Validate About, and Ligand. the error I get for replace residue is (get-monomer "Cd") (set-go-to-atom-molecule 1) debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook (generic-single-entry "Replace this residue with residue of type:" "ALA" "Mutate" (lambda (text) (using-active-atom (mutate-by-overlap aa-imol aa-chain-id aa-res-no text debug:: g.safe_scheme_command() with command (generic-single-entry "Replace this residue with residue of type:" "ALA" "Mutate" (lambda (text) (using-active-atom (mutate-by-overlap aa-imol aa-chain-id aa-res-no text (graphics-general-key-press-hook 67) debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook 67) Key 67 not found in (python) key bindings Key 67 not found in (scheme) key bindings (set-clipping-front 0.36) (set-clipping-back 0.76) (n-chains 0) (n-chains 1) (n-chains 2) (chain_id 2 0) (chain-n-residues "A" 2) (resname-from-serial-number 2 "A" 0) (n-chains 3) (chain_id 3 0) (chain-n-residues "A" 3) (resname-from-serial-number 3 "A" 0) (n-chains 4) (chain_id 4 0) (chain-n-residues "R" 4) (resname-from-serial-number 4 "R" 0) (n-chains 5) (chain_id 5 0) (chain-n-residues "R" 5) (resname-from-serial-number 5 "R" 0) (n-chains 6) (chain_id 6 0) (chain-n-residues "A" 6) (resname-from-serial-number 6 "A" 0) WARNING:: Null residue in mol_from_dictionary() for Cd WARNING:: Null mol from mol_from_dictionary() with comp_id Cd 1 get_monomer(): trying non-idealized: Cd WARNING:: Null residue in mol_from_dictionary() for Cd WARNING:: Null mol from mol_from_dictionary() with comp_id Cd 0 got imol -1 (get-monomer "Cd") 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] replace residue Cd not active
On 12/12/2022 15:49, Paul Kraft wrote: sorry, I am using Coot 0.9.8.5 EL (ccp4) on Ubuntu LInux 22.04 LTMD amd64, Ah, OK. Up to date. Good start. using the Replace Residue command under Edit or under Calculate-Modelling the command Cd does not function. Interesting. I think that you want to "Simple Mutate" (in the vertical toolbar). Replace Residue is a general purpose monomer superposition tool, the Simple Mutate tool is written with purines and pyrimidines in mind. Paul. 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] replace residue Cd not active
sorry, I am using Coot 0.9.8.5 EL (ccp4) on Ubuntu LInux 22.04 LTMD amd64, using the Replace Residue command under Edit or under Calculate-Modelling the command Cd does not function. thank you again, Paul 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] replace residue Cd not active
On 12/12/2022 15:09, Paul Kraft wrote: Hello, I am trying to mutate DNA, and can with Gd, Td, and Ad, but the Cd command is inopporative. Hello. I'm not a mind-reader. You need to start off with which version of Coot you're using and on which system (that matters less usually). You need to tell me what you pressed or clicked and what you expected to see and what actually happened. I searched the library list and found reference to Cd, but do not know why it is not working. Cd was using for DNA in Coot until about 2006 - so I am not sure what you're talking about. I did an end around by making a .cif from the smiles definition, That doesn't sound like the best solution. but when I use my definition it doesn't snap into place and it is a huge pain to move it into correct coordinates for it to bond correctly (especially since I do not have 3D goggle capabilities on this laptop) and need to do it for many cytidine mono phosphates. indeed... Paul. 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] replace residue Cd not active
Hello, I am trying to mutate DNA, and can with Gd, Td, and Ad, but the Cd command is inopporative. I searched the library list and found reference to Cd, but do not know why it is not working. I did an end around by making a .cif from the smiles definition, but when I use my definition it doesn't snap into place and it is a huge pain to move it into correct coordinates for it to bond correctly (especially since I do not have 3D goggle capabilities on this laptop) and need to do it for many cytidine mono phosphates. Please advise, Paul 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/
