Hi Hernando, Glad you got it to work, and thanks for pointing out the bug in the asymmetric unit placements in one direction along the helix. That was a weird bug caused by it doing a shift offset by half the correct angle and rise because the code was copied from Python 2 where division n/2 rounded to an integer while in Python 3 (which ChimeraX uses) it produces a float. So the bug happened when you used an odd number of copies n of the asymmetric unit. It is fixed in tonight's ChimeraX builds (dated October 10, 2024 or newer). Here is an example using the fixed code open 8wcm open 37443 from emdb measure symmetry #2 helix 15,90,5,opt minimumCorrelation 0.95 set true > Symmetry emdb 37443: Helix, rise 14.59, angle 83.44, center 128 128 128, n 5 sym #1 symmetry #2 > Made 5 copies for 8wcm symmetry #2 Tom 

On Oct 10, 2024, at 1:46 PM, Hernando J Sosa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks Tom

I got it to work but with some caveats:

measure symmetry #1 helix <aproxriseval>,<aproxanglevalue> set true

report the correct symmetry and the center in voxel units

Then doing :

sym #2 symmetry #1

kind of work but not completely: All the symmetry copies above the asymmetric unit model (model #2) are placed in the right place but the ones below are not.

However writing all the values explicitly in the sym command as:

sym #2 h,rise,angle,96,-64 center xc,yc,zc copies true

where the values rise and angle are as reported by the command measure symmetry #1 (96, and -64 are the ncopies and offset values in this example) and the center coordinates are the center also as reported by measure symmetry #1 BUT after multiplying the given coordinates (in pixels) by the pixel size (A/pix)

On another subject:

One feature of Chimera that was quite useful was the integrated idle IDE interface as it I allows to quickly run & test python scripts. Is there anything equivalent in ChimeraX? I have seen the instructions to create bundles and to manually set up the python evnviroment but this seems quite more complex that needed, if the objective is just to test a script and not necessarily to write a bundle. I have a bunch for Chimera python scrips that with minimal modification would work in ChimeraX.

Thanks

H.

From: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Sent: Wednesday, October 9, 2024 6:39 PM To: Hernando J Sosa <hernando.sosa@einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Center and Orient

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sym #3 H,8,120,10,-5

as indicated in the documentation

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html

Tom

On Oct 9, 2024, at 2:50 PM, Hernando J Sosa <hernando.sosa@einsteinmed.edu> wrote:

Also when tryng to give the symetry explicitly I get an error. Perhaps I am using the wrong syntax (??)

sym #3 sym-type H,8,120,10,-5 Expected a keyword

Thanks

H.

___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

From: Hernando J Sosa <hernando.sosa@einsteinmed.edu> Sent: Wednesday, October 9, 2024 5:41 PM To: Tom Goddard <goddard@sonic.net> Subject: Re: [Chimera-users] Center and Orient

I need to explicitly give the symmetry (helical) because the command

measure symmetry #1 set true (#1 is my map)

reports:

No symmetry found for my_map.mrc

H.

From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, October 9, 2024 12:32 PM To: Hernando J Sosa <hernando.sosa@einsteinmed.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Center and Orient

CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. Hi Hernando,

Here is how to apply symmetry to one copy of an atomic model in a symmetric cryoEM map in ChimeraX. First use the "measure symmetry" command to determine the map symmetry, then use the "sym" command to make the symmetric copies of the atomic model. Here is an example

open 8ofx open 16862 from emdb measure symmetry #2 set true sym #1 symmetry #2

Tom

<8ofx.png>

On Oct 9, 2024, at 7:52 AM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Thanks Elaine,

I will try to do this with ChimeraX. What I am trying to to do is to generate symetry related copies of a model fitted into a density map using the sym command. I noticed that the only way to define the center of symetry to be centered on the density volume was using the option center #n (where n is the id of the voume density) but only after doing center and orient by pressing the buttons in the volume viewer.

Although chimeraX is much more prowerful I still find hard to find the the equivalent in ChimeraX of some operations that I use often in Chimera. 😉

Thanks again,

Best

H.

_ From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Tuesday, October 8, 2024 5:04 PM To: Hernando J Sosa <hernando.sosa@einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> Cc: chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Center and Orient

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In Chimera, there may not be commands that do exactly the same thing as some button. You might look at "focus <model-number>" and "reset" (maybe only if one model is open, or they haven't been moved relative to one another?) but in my tests, they did not do exactly the same thing as those buttons.

That's one reason ChimeraX is way better than Chimera! You can use the GUI and it shows the command that it used in the Log.

Best, 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 Oct 8, 2024, at 1:38 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:

Dear Chimera,

What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab?

Thanks

H.

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