Hi Miguel, The "selRestrict" keyword only works on the selection (what is outlined with green). It sounds like you already figured out that the selection must be done in a separate command, since "hbonds" doesn't select atoms. The "spec" keyword can be used to specify a particular model but not anything smaller (i.e. not a particular residue or set of atoms, only the whole model), and it does not select anything. The remaining issue is how to prevent the selection outline from appearing. In MD Movie, the display is only updated after the per- frame script is executed, so you just need to add a command to turn off the selection after the hbonds are calculated: select :100 hbonds selRestrict cross relax false ~select If this was done in a command script outside of MD Movie, the way to suppress intermediate display is to string commands together with semicolons: select :100; hbonds selRestrict cross relax false; ~select (that should be all one line even if the annoying mail program breaks it up!) It does seem a bit inefficient to keep selecting/deselecting the same thing, but that is the only method I can think of currently. I will ask the others about perhaps adding a preference option to suppress the selection highlighting. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 7, 2008, at 6:40 AM, Miguel Ortiz-LombardÃa wrote:
I'm trying to follow hydrogen bonds in a trajectory from amber. To do so, I would like to run a 'per frame' script with something like:
hbonds spec :100 selRestrict cross relax false
However, this fails because apparently no atoms are selected. This fails as well:
hbonds spec #0:100 selRestrict cross relax false
I can only see the hydrogen bonds if insert a
select :100
before the hbonds command. I wouldn't like to see the green 'aura' of the selection, that's why I would like to make the selection within the hbonds command. I'm probably missing something, but cannot figure out what. Thank you!