Hi Guillaume,

  Opening the saved mmCIF file with an assembly will never automatically show the assembly in ChimeraX.  Seeing the assembly when you open the file indicates that your file contains all the coordinates for all of the subunits.  You should save the asymmetric unit (the original mmCIF file that symmetry was added to) in order to just include those atom coordinates.

Tom


On Nov 8, 2023, at 6:00 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote:

Thank you Tom.

It works for me too (both your example, and what I was initially trying to do). I realize now that I had managed to do what I wanted already. I was simply puzzled that the newly generated files opened with the assembly automatically displayed. I was expecting a single chain to be displayed until I request the assembly with the sym command or by clicking on the assembly ID in the log.

Cheers,

Guillaume

From: Tom Goddard <goddard@sonic.net>
Sent: Saturday, November 4, 2023 3:08:21 AM
To: Guillaume Gaullier
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] How to write biological assembly info in PDB or mmCIF?
 
Hi Guillaume,

  Adding the C7 symmetry to an mmCIF file is working for me in ChimeraX 1.6.  Here's an example with GroEL.

open 1080 from emdb
open 1grl
fit #2 in #1
delete ~/A
sym #2 C7 addmmcifassembly true
save test.cif
# If I now open the test.cif file in a text editor I see it wrote the symmetry matrices.
open test.cif
# Now the ChimeraX log lists the assembly as author defined assembly 3.  Apparently there were 2 previous assemblies in PDB 1grl.
sym #4 assembly 3

Not sure why it doesn't work for you.  Make sure to read the ChimeraX documentation so you understand what it is doing


Tristan Croll, the developer of ISOLDE, would probably have the best advice on how to refine a symmetric complex in ISOLDE.

  Tom



<testC7.png>
On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.

I can generate the other protomers with a command like this:

sym #1 C7 axis z center cofr

(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)

Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.

I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true
And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info.
I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.

Is there a way to do this? Or am I misunderstanding something?

Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).

Thank you in advance,

Guillaume









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