[Molvis-list] "Connect" between atoms of different models or Remove monitor label

Gian Garduque garduqueg at kenyon.edu
Thu Dec 9 16:06:26 EST 2010

I am constructing a tutorial about the SoxR protein (2ZHG).  This PDB file
is comprised of two models: I can use "select 1.1" or "select 1.2" to select
either of the two halves of the complex.  I am trying to show hydrogen bond
interactions at certain locations within the complex.  I do not think this
PDB file encodes hydrogen bonds because using the "hbonds" command does not
yield any results.  Therefore, I have been trying to show hydrogen bonds
using these two methods: 1) the "connect" command between two atoms or 2)
the "monitor" command between two atoms.  The problem with the "connect"
command is that I am unable to connect two atoms if they are from different
models (i.e. one atom is from 1.1 and the other is from 1.2).  Also, the
"connect" command only seems to work when I use "select atomno" and not when
I try to select two atoms using "select atomindex."  The issue with the
"monitor" command is that I am unable to turn off the distance label without
turning off the whole arbitrary bond.  If I were to use the "monitor"
command, it would be nice if I could remove the label so that it doesn't
look like I'm showing a distance measurement every time that I intend to
show a hydrogen bond.  Are there any solutions out there to these issues?

Thank you,
Gian Garduque
Kenyon College
Gambier, OH

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