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 * 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)