Re: [COOT] odd observation

On 12/12/2022 16:29, Paul Kraft wrote: just needed to close the old sequence view and open a new one to see the updates. Thanks for your extremely prompt help. [...] Using simple mutate it seems I must close and reopen the sequence viewer for it to update the sequence even though it is clear

[COOT] odd observation

nooo just needed to close the old sequence view and open a new one to see the updates. Thanks for your extremely prompt help. I am curious as to why the replace residue worked for the others and when I used "replace residue" with Gd, Td, or Ad ...it updated the sequence view immediately. Using

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-JIS

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:: bac

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 (g

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

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

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

[COOT] mutating DNA Cd command non functional

hello, I am trying to mutate dsDNA and can with Gd, Td, and Ad, but not Cd. I search the library list and found reference to Cd, but can't figure our why the command doesn't work. I did an end around by making a ligand CTD.cif using the smiles definition but it doesn't snap into the correct orie

[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'