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01 Show the ChimeraX working directory
pwd02 Open a pdb file in the working directory
open asu.pdb03 Close a structure
close #1 # close one structure
close all # close every structure04 Export the current selection
save lamarck.pdb selectedOnly true05 Export the structure as a png with a transparent background
save lamarck.png transparentBackground true06 Select residues on a chain
select #1/A:100-200 # select a contiguous range
select #1/A:100,150,200 # select discrete residues
select ~sel # invert the selection07 Split a model by chain
split #108 Delete residues to break a chain
delete #1/C:72 # delete one residue
delete #1/C:72-78 # delete a contiguous range
delete #1/C:72,75,78 # delete discrete residues09 Adjust the transparency of the selection
transparency sel 60 target ac # a = atom, c = cartoon; both are changed01 Find neighboring residues
select zone #1/C:260-268 5 # select residues within 5 Å of the target segment02 Superimpose model1 onto model2 (to inspect mutations or differences; the log reports the RMSD automatically)
mm is the short form of matchmaker
mm #3 to #1To pair chains manually: the default pairing bb picks only the single highest-scoring pair of chains, so a multi-chain complex needs pairing ss to state the pairs explicitly
mm #2/B,C to #1/A,B pairing ss # #2/B onto #1/A and #2/C onto #1/B, both pairs fitted together
mm #2/B,C to #1/A,B pair ss bring #3 # move #3 along with #2The two sides must name the same number of chains, matched in the order written. The whole of #2 then moves as a rigid body; the named chains only determine which residues take part in the fit.
03 Cycle automatically through dozens of open structures
perframe drives the cycling; $1 is substituted with each number from range in turn
perframe "hide models; show #$1 models" range 1,24 interval 120 # 24 models, switching every 120 frames
perframe stop # stop cycling