Hi Joel, You may need to use the "copies true" option of "sym" to make the copies as full atomic data instead of graphical clones. See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 3, 2025, at 10:31 AM, Joel Gallardo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

to whom it may concern,

i have mapped out a mol2file onto a structure found in a .mrc file. and then i ran this command to multiply the mol2 structure: sym #2 h,0.357979,132.83196,72,-40 coord #1 center 119.04,119.04,119.04 it multiplied it as intended which is good but now i want to save those multiplied mol2 files into a sperate mol2 files. i tried this command: save multiplied_structures.mol2 format mol2 models #2 but this only saves a single mol2 structure into the new mol2 file. i want all 72 molecules in one mol2 file.

can you give me some advice as to how i may be able to do this? my ultimate goal is to take that mol2 file and do an md simulation.

Best, Joel Gallardo (Graduate student in chemistry)

Hi Joel, That sym command already makes each copy a separate model. I.e. if the output structure with all the copies is #3, then the individual copies are models #3.1, #3.2, etc. You can look in the Models list to see the exact numbers (click the disclosure triangle to expand any model to its sub-models). So you could do 72 save commands, one for each of those sub-models, #3.1, #3.2 etc. in my example. save blah01.mol2 models #3.1 relModel #3.1 save blah02.mol2 models #3.2 relModel #3.1 [...] To make sure they retain their spatial relationships, each save would be relative to the same model (same relModel number for all save commands) although it doesn't matter which one. See "save" help for command options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mol2> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 3, 2025, at 1:04 PM, Joel Gallardo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

thank you for the advice i was able to get the mol2 with all the drugs in them using the command :

sym #2 h,0.357979,132.83196,72,-40 coord #1 center 119.04,119.04,119.04 copies true

do you know ho i may be able to save each clone as seperate mol2 structures?

best,

Joel GallardoFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 3, 2025 1:41 PM To: Joel Gallardo <Joel.Gallardo@csi.cuny.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] saving cloned structures on chimerax inquiry * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *

Hi Joel, You may need to use the "copies true" option of "sym" to make the copies as full atomic data instead of graphical clones. See:

<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Apr 3, 2025, at 10:31 AM, Joel Gallardo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

to whom it may concern,

i have mapped out a mol2file onto a structure found in a .mrc file. and then i ran this command to multiply the mol2 structure: sym #2 h,0.357979,132.83196,72,-40 coord #1 center 119.04,119.04,119.04 it multiplied it as intended which is good but now i want to save those multiplied mol2 files into a sperate mol2 files. i tried this command: save multiplied_structures.mol2 format mol2 models #2 but this only saves a single mol2 structure into the new mol2 file. i want all 72 molecules in one mol2 file.

can you give me some advice as to how i may be able to do this? my ultimate goal is to take that mol2 file and do an md simulation.

Best, Joel Gallardo (Graduate student in chemistry)