swapaa #!1$i same criteria 10000 rotLib Dunbrack retain true

exit" > GenerateRotamers1.cxc

chimerax --nogui GenerateRotamers1.cxc >> GenerateRotamers1.log 2>>GenerateRotamers1.err

while read -r resid rotamers; do

        # Generate a comma-separated list of numbers from 1 to $rotamers

    criteria=$(seq -s, 1 $rotamers)

    echo "

open $1

swapaa #!1:$resid same criteria $criteria rotLib Dunbrack retain true

sel #1:$resid

sel ~sel

del sel

save resid_$resid.pdb

exit

    " > GenerateRotamers2.cxc

From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Thursday, September 5, 2024 6:38 PM
To: Alexander Lee <Alex.H.Lee@outlook.com>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Select multiple rotamer conformations for a single amino acid

Hi Alex,

The Rotamers tool logged a swapaa command when you did that, and that command does indeed do the same thing as the tool.  The critical command argument in this case is “criteria” followed by a comma-separated list of integers.  Criteria is documented to either be a string indicating how to “tie break” rotamers (density fit, clash score, # H-bonds, or highest prevalence) or an integer indicating that the Nth highest-prevalence rotamer should be used.  What isn’t documented is that it can also be a comma-separated list of integers, in which case the corresponding rotamers will be added as alt locs.  It probably didn’t get documented because it seemed to only be useful in the context of the tool, because there is no easy way of knowing how many rotamers there are for a particular residue-type / backbone-configuration combo.  Nonetheless, I guess it would be safe to just use the top two (or possibly three) rotamers outside the context of the tool.

We will be documenting this additional criteria mode.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab