Thank you for your replies. 1- Indeed the map shifted to the grid point 270 270 244 when I used the command Volume originalindex, however the following problems occurred: - I originally fit my monomer relative to the map location before being shifted to the original position...so now the monomer is out of place.....is there a way I can move it with the map...or into the map without having to fit it again manually??? - When I used the sym C15 command, I got, as before, 15 visual copies of the monomer, but they are still not in the map and I feel that visually, the map is not in the center of that formation either. I attached a screenshot to show that. 2- I indeed got the right symmetry when I used the nMax command, so thank you so much. As for the copy command, so I should type something like copy true #2 (the model) C15??? I am sorry for the many questions. I am still a beginner user of ChimeraX and I read the sym command help page of course before I emailed you but it is still hard to get for me. Noha On Fri, May 17, 2024 at 4:37 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Noha,
I suggest you set the center of symmetry of your map to grid point 270,270,244 as indicated by the measure symmetry command (that found only C3 symmetry) using
volume #2 originIndex 270,270,244
then the sym command
sym #2 C15
will get the correct center of symmetry (which defaults to x,y,z = 0,0,0). The reason the sym command gave the wrong placement is because the origin of the map is probably specified at the lower left front corner of the map box in the map file. So the above command changes where ChimeraX considers the origin so it is at grid index 270,270,244.
The reason the measure symmetry command found C3 instead of C15 is because that command only searches for cyclic symmetries up to C8 unless you specify the nMax parameter. So the following might work
measure symmetry #2 nMax 15
This is explained in the documentation
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry
In any case, the 3-fold symmetry is a subsymmetry of 15-fold so the origin it is reporting should be correct.
Tom
On May 16, 2024, at 9:16 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Noha,
(1) you probably need to specify the center and maybe also the axis in your "sym" command. This command has "center" and "axis options, see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry>
The hard part is figuring out what your center and axis are, if you don't already know. The "sym" command also has an option "copy true" if you want full atomic copies instead of graphical clones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
(2) "measure symmetry" may help figure out the center and axis needed by "sym", but it is only a guess and it assumes your data are in a standard orientation. If the map is not in a standard orientation and maybe not centered where it expects, it would not be able to detect the symmetry correctly. Another reason for errors is noise in the data. See "measure symmetry" and its options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 16, 2024, at 1:54 AM, Noha Elhosseiny via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I have a map with C15 symmetry in which I already refined the fitting of a single monomer (asymmetric unit) in the map using coot. I now want to generate the complete 15-mer atomic model. I watched your tutorial : ( https://youtu.be/v3jI43YJQMg?si=WeQg2ef2MPOw2J7H) and I tried to use the command "sym #2 (my model) C15 to do that, but instead of getting the monomers fitted around the axis of symmetry, I could see that 15 versions were visible but in a circular circumference around my map, away from the center, and the monomers are widely spaced from one another. I kind of expected this because I did not specify any coordinates to do this copying, so how can I fix this?
Another question: when I use the command "measure symmetry" I get "C3, center 270 270 244". So I do not understand why it's detecting a C3 when it's clearly a C15. I think the above coordinates of the center can be used to solve my fitting problem but I am not exactly sure how.
Finally I understood that even if the monomers appear properly fitted, given I manage to do it, that these are just graphical copies. So how can I then make real copies of the graphical representation of the 15-mer?
Thanks
Noha
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-- *Noha M. Elhosseiny, PhD* Department of Microbiology & Immunology Faculty of Pharmacy, Cairo University. Kasr El-Ainy St, Cairo, Egypt, 11562- Lab C-407 Website: https://eg.linkedin.com/in/nohaelhosseiny <https://eg.linkedin.com/in/nohaelhosseiny>
