[Chimera-users] A question abount "define axis"

[Elaine Meng]

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

> On Feb 6, 2023, at 8:11 PM, squirrel via Chimera-users <chimera-users at 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
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