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

[Tom Goddard]

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 at 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
> -----
> 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
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
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