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Re: Missing bond between some atoms in VMD

dummy@example.com (SCmwfnQ) — Mon, 07 Nov 2022 15:05:50 +0000

Also, VMD Dynamic Bonds can add bonds based on interatomic distances.

Re: Missing bond between some atoms in VMD

dummy@example.com (sobereva) — Sat, 08 Oct 2022 09:36:21 +0000

You are right, when bond path is displaying, user may accidently click a point in bond path rather than nucleus.

Re: Missing bond between some atoms in VMD

dummy@example.com (rkia) — Fri, 07 Oct 2022 14:36:16 +0000

Dear Prof. Lu,

I found an easier way to make missing bonds between some atoms. One someone run "source aim.vmd" and then "source igm_inter.vmd" and saw some missing bonds it is easier to remove the "bond paths" between atoms from graphics menu and then make the missing bond and then again activate the "bond paths".

Regards,
Reza

Re: Missing bond between some atoms in VMD

dummy@example.com (rkia) — Mon, 29 Aug 2022 07:18:33 +0000

Dear Prof. Lu,
many thanks.
Reza

Re: Missing bond between some atoms in VMD

dummy@example.com (sobereva) — Mon, 29 Aug 2022 05:51:09 +0000

Dear Reza,

After choosing "add/remove bond", you must click exactly centers of two atoms, so that the atoms can be selected.

Best,

Tian

Missing bond between some atoms in VMD

dummy@example.com (rkia) — Sun, 28 Aug 2022 03:51:48 +0000

Dear Prof. Lu,
I obtained the output of AIM and IGM routines and put them in VMD for visualization by source aim.vmd and source igm_inter.vmd for a metal complex. Some of the bonds are missing in VMD and I tried to make the bond between those atoms via "Mouse" and "addd and remove bond" in VMD but it doesn't work. Could you please guide me.

Regards,
Reza