Problems with topotools setbond list

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1

Hi,

Recently I found that the topotools very useful. Follow the instructions, however, I found that the setbondlist command does not work properly,
Here is the test. Generally, I have tried different input patterns for setbondlist but neither of them works. It would be really great if there is just ONE example shows how to use this command.

Main console display active (Tcl8.5.6 / Tk8.5.6)
(VMD) 1 % set sel [atomselect top all]
atomselect0

Main< (VMD) 2 $sel num 60 Main< (VMD) 3 $sel list
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
Main< (VMD) 4 topo clearbonds -sel $sel Main< (VMD) 5 topo getbondlist -sel $sel
Main< (VMD) 6 topo addbond 1 2 -sel $sel Main< (VMD) 7 topo addbond 3 4 -sel $sel
Main< (VMD) 8 topo getbondlist -sel $sel {1 2} {3 4} Main< (VMD) 9 topo setbondlist {5 6} {7 8} -sel $sel
0
Main< (VMD) 10 topo getbondlist -sel $sel Main< (VMD) 11

Best
Ming

2

Hi,

Recently I found that the topotools very useful. Follow the instructions, however, I found that the setbondlist command does not work properly,
Here is the test. Generally, I have tried different input patterns for setbondlist but neither of them works. It would be really great if there is just ONE example shows how to use this command.

It works properly. It is your understanding of Tcl that doesn’t. You are not providing a list of bonds as argument. The documentation explains it. For the rest I’d rather suggest you practice handling lists in Tcl a bit more. The Tcl tutorial on www.tcl.tk will do wonders …

Axel

3

Thanks!~ I will look at the tutorials :slight_smile:

Best
Ming