[Chimera-users] question

Tom Goddard goddard at sonic.net
Thu Apr 18 09:10:08 PDT 2013

I don't understand what you are trying to do.  My best guess is you have 
a symmetric trimer crystal structure and you want to fit a monomer of 
that atomic model into a 5-fold symmetric map.  To do that I would open 
the trimer atomic model, delete all except one monomer, fit it into one 
of the 5 equivalent positions in the map, then use the "sym" command to 
make the other 4 symmetrically placed copies.  If I wanted to reduce 
clashes I'd assign c5 symmetry to the map as described before and use 
the "fitmap" command with the symmetric fitting option.

The "volume #0 symmetry c5" command doesn't give any error message like 
"can't find symmetry".  So I'm not sure what problem you are having.  
You need to explain it more clearly.


> Tanks  for your kindly answer!But i use the command volume #0 symmetry 
> c5,it tell me that cann't find the semmetry. The map is made from 
> crystal structure using "fit in map".it a trimer,i want to impose 
> 5-symmetry in order to fit with my map.
> At 2013-04-17 05:43:04,"Tom Goddard" <goddard at sonic.net> wrote:
>     How about the Chimera command
>         volume #0 symmetry c5
>     The symmetry assigned to the map isn't used for much in Chimera. 
>     It can be used for symmetric fitting but if you tell it the wrong
>     symmetry you will just get nonsense fits.  The other main use of
>     symmetry is to replicate PDB models with the sym command.  There
>     you can specify the symmetry with command options.  So I can't
>     think of any reason you would use the above command.
>     http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html
>     http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions
>       Tom
>>     Dear sir
>>         I have some question in using your excellent Chimera.
>>        How can i set 5 symmetry to a 3 symmetry map?
>>     thank you

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