[chimerax-users] Mutated several residues (amino acids or nucleotides) at the same time

[Vorländer,Matthias Kopano]

Dear Elaine, 

Thanks a lot for your reply. I was unaware that modeler can be used directly from within chimeraX, that's great. 

Regarding the possibility to replace multiple residues to a different sequence using the swapna and swapaa commands, a text file is a workaround, but I think the implementation of a native feature would be a valuable addition for everyone who works with ChimeraX and Isolde for model building :) 

Many thanks,
Matthias


On 08.03.23, 17:29, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Matthias,
    You can already change multiple residues using a single "swap" command, but only if they will be the same final type.  For example, something like:

    swapaa :phe,tyr his
    - or -
    swapaa /A:1-4 leu

    If you want to model a specific protein sequence that has a lot of differences from the original structure, but using that original structure as the template, the better approach would be with Modeller comparative modeling.  That cannot be used for nucleic acids, however.
    <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>

    I.e. you would open the target sequence, make sure to associate it with the original structure if it is not already automatically associated, and then use the Modeller Comparative tool or "modeller comparative" command. 

    <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#sequence>
    <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#association>
    <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>

    There are also AI prediction methods for peptide structure, e.g. "alphafold predict" "esmfold predict" albeit with better reliability on natural sequences rather than newly designed.
    <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>
    <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html>

    If you need to stick with multiple "swap" commands (e.g. for nucleic or other reasons) it may be easier to create a command (.cxc) file in a text editor first and then simply open it to execute.
    <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>

    I hope this helps,
    Elaine
    -----
    Elaine C. Meng, Ph.D.                       
    UCSF Chimera(X) team
    Department of Pharmaceutical Chemistry
    University of California, San Francisco

    > On Mar 8, 2023, at 1:50 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
    > 
    > Hi there, 
    >  
    > I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes. 
    >  
    > Many thanks,
    > Matthias