Your error message "Must specifiy at least two atoms/centroids to define an axis" comes from the define axis command and means your define axis command specified 1 or 0 atoms. Based on your other commands I would guess that means that at least one of your select commands did not select anything.

Tom

On Feb 7, 2023, at 9:13 AM, Elaine Meng via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Hello, My only guess is that maybe you used the same model id more than once and you have multiple markers in that model. For example if you do this command 2 times

measure center :1.A mark true model 1

...then you will have 2 markers (atoms) in #1. So you have to make sure that first you close all the previously created marker models and then make only one marker in each one.

Also you don't need an extra selection step, you can just say what you want to measure center in the command directly, as in my example above.

These commands work fine for me:

open 4hhb measure center :1.A mark true model 1 measure center :1.B mark true model 2 measure center :141.A mark true model 3 measure center :146.B mark true model 4 dist #1 #2 dist #1 #4 dist #1 #3 define axis name my_axis #2 #4 [... etc ...]

I hope this helps, Elaine

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

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On Feb 6, 2023, at 8:11 PM, squirrel via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Dear Chimera list, I'm Interested in finding and showing the distance of N-terminal and C-terminal between two proteins. As I can't download GUI so I use "chimera --nogui" to compute them. That's my command: open protein.pdb sel:1.Ln; measure center sel mark True radius 0.3 color cyan modelId 1;

sel:1.S2;

measure center sel mark True radius 0.3 color cyan modelId 2;

sel:390.Lz;

measure center sel mark True radius 0.3 color cyan modelId 3;

sel:44.LH;

measure center sel mark True radius 0.3 color cyan modelId 4;

distance #1 #3;

define axis name Ln_N_Lz_C #1 #3;

distance #1 #4;

define axis name Ln_N_LH_C #1 #4;

distance #2 #3;

define axis name S2_N_Lz_C #2 #3;

distance #2 #4;

define axis name S2_N_LH_C #2 #4;

stop

But I found that when I input "distance" and "define axis" the terminal shows that "Must specifiy at least two atoms/centroids to define an axis". <1675742867493.png>

I am puzzle because I can see the #1,#2,#3，#4 in the list. <1.png>

Can you give me some guidance?

Thanks in advance _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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