[chimerax-users] deleting sidechain in ChimeraX

[Joel Meyerson]

Hi Elaine,
This is just what I needed. The "&" operator is what I was missing. Unless I'm mistaken, deleting side chains with this approach is equivalent to adding stubs in COOT, but it's very convenient to do this at the ChimeraX command line. Thank you for the help.

Best,
Joel

On 4/20/20, 6:42 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Joel,
    The command to delete atoms is "delete" ... mainly need to consult the documentation on how to specify the set of atoms that you want, considering that it's not "undo"able!
    
    <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_delete.html&d=DwIFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=KpRBeplTtj-tmPfI_faeWtxlTnlU_9FhUVDKBysqkos&s=Yn3bX1Sd-kaHR0ecm0j34aflDHuQR3fnB5v8HZnJe9E&e= >
    <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_atomspec.html&d=DwIFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=KpRBeplTtj-tmPfI_faeWtxlTnlU_9FhUVDKBysqkos&s=fdXkPW18bGVzRxVtpErqc6HbHmrscBRyDweu58oSjnM&e= >
    
    Something like:
    
    delete #4/A:4-45,53,80-90 & sideonly
    
    However, to check your atomspec before deleting you may want to check it with select first instead of delete:
    
    select #4/A:4-45,53,80-90 & sideonly
    delete sel
    
    ...assuming you don't want to delete CA atoms. #4 is model 4, /A is chain A (case only important if you have both upper- and lowercase), and then the stuff after : is residue numbers and ranges.  If you wanted to delete CA atoms also, it would be "sidechain"  instead of "sideonly" (this is so that "show sidechain" will actually connect the sidechain display to ribbon instead of having just CB onward floating in space).
    
    These things are all described in that "atomspec" page linked above, which is admittedly long because there are several different ways of specifying atoms or other models.
    
    Also you could use the Sequence Viewer to select residues by dragging a box around them
    <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_tools_sequenceviewer.html&d=DwIFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=KpRBeplTtj-tmPfI_faeWtxlTnlU_9FhUVDKBysqkos&s=KmO7qs0Fp6-4gahsReN2gqFhctavAWC_i3fIFU5Xzkw&e= >
    
    ...and then intersect with sidechain in the delete command:
    
    delete sel & sideonly
    
    I hope this helps,
    Elaine
    -----
    Elaine C. Meng, Ph.D.                       
    UCSF Chimera(X) team
    Department of Pharmaceutical Chemistry
    University of California, San Francisco
    
    > On Apr 20, 2020, at 4:29 PM, Joel Meyerson <jrm2008 at med.cornell.edu> wrote:
    > 
    > Hi,
    > What is the command or sequence of commands which can be used to delete the sidechain on an amino acid or range of amino acids? I reviewed the ChimeraX atom spec page but could not find a way to do this.
    > 
    > Thanks,
    > Joel