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 -- *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>
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
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- *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>
Hi Noha, As for your issue #2, the "copies true" option that I recommended in my previous message (I accidentally said copy but it is "copies") should go into the "sym" command that creates the copies in the first place.
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>
You would not use the separate "copy" command, which has a different function. However, you would first need to figure out your issue #1 so that the copies will go where you want them. Elaine
On May 16, 2024, at 7:19 PM, Noha Elhosseiny via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- 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 <Screen Shot 2024-05-17 at 11.10.16 AM.png>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Noha, When you have a map with symmetry it is pretty useful to put the origin of coordinates at the center of symmetry. If you fit your atomic model without doing that then you run into the problems you have discovered. You can move your atomic model after setting the origin of the map. You'll have to first figure out what the original origin grid index is (menu Tools / Volume Data / Map Coordinates), probably 0,0,0. Then you shifted it to 270, 270, 244 so if your voxel size is say 1.2 Angstroms them you need to shift your atomic model by -270*1.2, -270*1.2, -244*1.2 for example with command move -324.0,-324.0,-292.8 model #1 assuming your atomic model is #1. Then the "sym #2 C15 copies true" command should put the copies in the correct location. But it could be the 270,270,244 origin is slightly off. You can read the measure symmetry documentation to learn why that can happen. A way I often use to test if the origin is correct is to rotate the map about the center of symmetry and see if it wobbles turn z 24 frames 150 model #2 Here I turn it by 24 degrees in 150 steps to do 10 full 360 degree rotations and I visually see if it wobbles. Ideally this nonsense would not be necessary if the map file was originally written by the reconstruction software that imposed the symmetry to put the symmetry origin at 0,0,0. Or if you ran the reconstruction software and know the exact center of symmetry. Unfortunately the center information is often lost and you have to resort to these tricks to try to figure out where it is. Tom
On May 16, 2024, at 7:19 PM, Noha Elhosseiny via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 <mailto: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 <mailto: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 <mailto: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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- 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> <Screen Shot 2024-05-17 at 11.10.16 AM.png>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Elaine, Thank you very much for the clarification. I figured it out after reading your reply and revising the help page several times. It is obvious but this is my first time using command line in ChimeraX so its not easy for me. I really appreciate your help. Noha
Dear Tom, That worked beautifully. I cannot thank you enough for your thorough explanation. Noha
participants (4)
-
Elaine Meng -
Noha Elhosseiny -
noha.elhuseiny＠pharma.cu.edu.eg
-
Tom Goddard