VMD-L Mailing List

From: Lukáš Pravda (xpravda_at_ncbr.muni.cz)
Date: Tue Oct 29 2013 - 04:40:29 CDT

Dear all, I'm fairly new user to VMD (win32 v. 1.9.1) and I would like to
create a custom molecule in VMD using tk scripting. I have found several
tutorials for that purpose, however, none of them works fine for me. Let say
I'd like to create a molecule of 3 atoms with given radius.

 

Now I'm doing something like this

 

set m [mol new atoms 3]

mol top $m

set atom [atomselect top "index 0"]

$atom set {x y z} {{1.0 2.0 3.0}}

$atom set radius 1.4

set atom [atomselect top "index 1"]

.

mol delrep 0 $m

mol representation VDW 1.000000 18.000000

mol color Name

mol selection {all}

mol material Opaque

mol addrep top

mol selupdate 0 top 0

mol colupdate 0 top 0

mol scaleminmax top 0 0.000000 0.000000

mol smoothrep top 0 0

mol drawframes top 0 {now}

 

Command for setting x y z coordinates passes without any errors, however,
when retrieving the new value with $atom get {x y z} command nothing changes
and it's coordinates are still the default {0.0 0.0 0.0}. Moreover not even
a single sphere is drawn. Do you have any idea what am I doing wrong?

 

Thank you for any piece of advice

 

Lukas