[chimerax-users] How to display crystal packing?

[Guillaume Gaullier]

I need to measure distances between the main model’s atoms and atoms in the symmetry copies, and I also need to be able to tweak the representation (cartoon, sticks, colors, etc.) in any way ChimeraX will allow independently between the main model and the symmetry copies.

Guillaume


> On 8 May 2020, at 15:54, Tristan Croll <tic20 at CAM.AC.UK> wrote:
> 
> The symmetry display in ISOLDE is actually provided by the Clipper plugin (which I’m also responsible for). It doesn’t currently have a built-in command to turn the symmetry views into real atoms, but it wouldn’t be particularly difficult to add that. Is actual copies of the molecules what you want? Or are instanced “ghost” copies of the main molecule sufficient?
> 
> 
> 
> 
>> On 8 May 2020, at 14:24, Guillaume Gaullier <guillaume at gaullier.org> wrote:
>> 
>> Hello,
>> 
>> Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do.
>> 
>> What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions?
>> 
>> It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX).
>> 
>> Thank you in advance,
>> 
>> Guillaume
>> 
>> 
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