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 Gallardo
From: 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
 
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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/commands/sym.html*copies__;Iw!!Jg5O23S-og4!6Re5givD_B6afGD7sMydCtITQxMB7v5ez_Z1D0DgjaJ-15SdEoYzr-1kaGiTYexfqQoEyLHqHIi6hl8N4Ep1UbMg$ >

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)