[Chimera-users] make helical filament model using command sym

[Elaine Meng]

Hi Yaowang,
This format of your command looks correct for specifying the rise,twist,n yourself:

> sym  #0  group  h,2.292,179.6,100 coord #1
… or ...
sym  #0  group  c2*h,2.292,179.6,100 coord #1

(the second one if you need c2*h instead of just h).  There are similar examples in the “sym” manpage:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

However, I don’t know which of those you need, or what rise and twist values are needed to give the result you want.

I don’t think there is a way to specify “n” copies if you are using the symmetry of another model, sorry.
> sym  #0  group #1

If you save the map in Chimera map format it includes the symmetry, but then you would have to interpret the file contents to get the rise and twist to use in a “sym” command where you specify “n” yourself.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#save>

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


> On Jun 12, 2018, at 11:35 PM, Yaowang Li <liyaowang2911 at gmail.com> wrote:
> 
> Dear all,
> 
> I have built a model from cryo-em density map, now I am going to create a model of a filament (have a length of the pitch, over 1000 A) from it.
> 
> I think the command 'sym' can do it, but not easy for me. I have tried many times.
> 
> sym  #0  group  h,rise,twist,100
> 
> or 
> sym  #0  group  c2*h,rise,twist,100 coord #1
> or
> sym  #0  group  h,2.292,179.6,100 coord #1
> 
> the model is wrong
> 
> <image.png>
> 
> 
> I also try to measure the symmetry first 
> and 
> sym  #0  group #1
> <image.png>
> 
> 
> it is almost right, but I need much longer, how set it? using the 'n' parameter? and how?
> and if I want to set rise and twist myself, how to do it?
> 
> 
> 
> Best wishes, 
> 
> 
> Yaowang
> 
> 
> 
> 
> 
> 
> 
> 
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