Dear Tom,

Thank you very much for those useful information.

Combining all given information, I confirm this command helped me generate chains that "automatically" fit into my density:

      sym #1 H,4.75,1.4,20 center #1 axis z 
      (the "axis z" is option in my case too)

For Elaine suggestion about the center, one can look up the unit cell of the density (I use Coot, but I am sure ChimeraX should have one too), and whatever the number of unit cell that you have, the input is ½ of those number. e.g. The unit cell (x, y, z) is (248.4, 248.4, 248.4), then the input will be like this:
      sym #1 H,4.75,1.4,20 center 124.2,124.2, 124.2


Both of those commands work for me.

Thank you again for helping.

Best,

B

From: Tom Goddard <goddard@sonic.net>
Sent: Thursday, July 11, 2024 12:24 PM
To: Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Generating long fibrils
 
Hi Binh,

  A few more useful sym commands.  To use the center of the model as the center of the filament

sym #1 H,4.75,1.4,20 center #1 axis z

The sym command does not copy the atoms by default it just makes graphical copies when more than 12 copies are needed.  You can get rid of the graphical copies with

sym clear #1

And to get real copies use the "copies true" option

sym #1 H,4.75,1.4,20 center #1 axis z copies true

  Tom


On Jul 11, 2024, at 10:20 AM, Tom Goddard <goddard@sonic.net> wrote:

Hi Binh,

  Here's an example using the sym command to make helically arranged copies of a structure 

open 9eoe
sym #1 H,4.75,1.4,20 center 0,0,0 axis z

The syntax from the documentation is

sym #model-num H,rise,angle,n[,offset]

where rise is in angstroms, rotation angle is in degrees, and n is number of copies


  Tom

On Jul 11, 2024, at 10:02 AM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Awesome, thank you very much Elaine. 

From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Thursday, July 11, 2024 12:00 PM
To: Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Generating long fibrils
 
EXTERNAL MAIL

Following onto Oli's answer (thanks!), the ChimeraX "sym" command does allow building additional copies with helical symmetry:

<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html*symmetry__;Iw!!MznTZTSvDXGV0Co!H3NHtSe0HnpIAH7BgjMtwLlabtMS9TlWHiAEzBEhKL51L0B1C_jI4hZk4oSPIveRPsDGa-wazRtm8Aws9euEnujAHHJ8$ >

The tricky part is figuring out what you need to put in the "sym" command for the axis and center, in addition to the helical parameters.

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

> On Jul 11, 2024, at 9:10 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> The server seems to be down right now, but it is possible you could also do this using the sym command in ChimeraX (I'm just not sure whether there are options for helical or only point group symmetry):
>
> https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html__;!!MznTZTSvDXGV0Co!H3NHtSe0HnpIAH7BgjMtwLlabtMS9TlWHiAEzBEhKL51L0B1C_jI4hZk4oSPIveRPsDGa-wazRtm8Aws9euEnpThIkFe$
>
> Cheers
> Oli
>
>> On Jul 11, 2024, at 12:09 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
>>
>> Hi Binh,
>>
>> There may well be a way to do this with ChimeraX, but you can also easily use servalcat for this:
>>
>> https://urldefense.com/v3/__https://servalcat.readthedocs.io/en/latest/spa_examples/ab42.html*generate-symmetry-copies__;Iw!!MznTZTSvDXGV0Co!H3NHtSe0HnpIAH7BgjMtwLlabtMS9TlWHiAEzBEhKL51L0B1C_jI4hZk4oSPIveRPsDGa-wazRtm8Aws9euEnnIQ1x6v$
>>
>> Cheers
>> Oli
>>> On Jul 11, 2024, at 12:02 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>>
>>> Dear all,
>>>
>>> Is there a way in chimeraX that I can use to generate a long fibril, say 20 chains, from a single chain with a twist angle of -1.4 degree and the rise (distance between layers) of 4.75 Angstrom. Some thing like this:
>>> <image.png>
>>>
>>> I normally used Coot and manually add a single layer into density.
>>>
>>> Thanks,
>>>
>>> B
>>>
>>>

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