[chimerax-users] using sym to generate assemblies

[Elaine Meng]

Hi Natalie,
AllI can do is repeat the message: your data does not have the assembly that you specified.  It is impossible to be more specific without knowing exactly what data and command you used.

If your data is an entry from the Protein Databank, for ChimeraX to read the assemblies you have to open it as mmCIF format.  Then, if there are assemblies defined, they will automatically be listed in the Log when you open the file, as described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#assembly>

Or as mentioned in that link, you can use "sym <model-number>" to report the available assemblies, e.g. if your structure is model #1:

sym #1

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

> On Nov 19, 2022, at 7:26 PM, Natalie Loui via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi all, 
> 
> I’m trying to visualize a capsid by using the sym command but I keep getting this error ”Assembly "1" not found, have"
> 
> If you have any advice, please let me know. 
> 
>   Natalie Loui
> PhD Student | Skaggs Graduate School of Chemical and Biological Sciences
> Email: nloui at scripps.edu | Phone #: (808)221-8270 
> Scripps Research Institute | 130 Scripps Way, Jupiter, FL 33458 | https://education.scripps.edu