From: Rajorshi Chattopadhyay (
Date: Tue Apr 11 2023 - 15:21:54 CDT

Dear all,

I am trying to make a visualisation of my simulation trajectory that
contains La, Cl ions in an aqueous solution. I want to draw bonds
between the La and those Cl ions which are in the first coordination shell,
for all the frames.

I tried this out by creating two separate groups of atoms, one
containing the La ion and the other containing the coordinating Cl ions. I
have then used the DynamicBonds drawing method to draw bonds between the
two groups. I find that this creates bonds correctly between the La ion and
Cl ions, but extra bonds between the Cl ions that are within the set cutoff
are also drawn. Relevant portion of the tcl script is as follows:

atomselect macro hyd {name H}

atomselect macro oxy {name O}

atomselect macro cl {name Cl}

atomselect macro na {name Na}

atomselect macro clcoord {cl within 3.8 of name La}

mol representation VDW 0.500000 21.000000

mol color Name

mol selection {name La}

mol material Opaque

mol addrep top

mol representation VDW 0.300000 20.000000

mol color Name

mol material Opaque

mol selection {clcoord}

mol addrep top

mol selection {name La or clcoord}

mol representation DynamicBonds 3.50000 0.150000 15.000000

mol addrep top

Is there a way to remove these extra bonds between the Cl ions ? I thank
you in advance for your help/suggestions.

With Regards,
Rajorshi Chattopadhyay,
PhD Researcher in Mineralogy/Crystallography,
Institut für Geologie und Mineralogie,
Universität zu Köln, Germany