On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:

In the "Define script.." I defined "select ligand z<10", then OK and a BUG

window was presented. Attached is the reply log (bug). I tried with z<4 with

the same result (actually, I don't remember if attached bug file refers to z<10

or z<4).

In the script-definition dialog you need to have "Interpret script as" set to "Chimera commands". You had it set to "Python".

Still found difficulties in loading more than one mdcrd, though this should be
my fault. I was not sure if the list of mdcrd is to be given at beginning or if
the other mdcrd files after the first one are to be given subsequently from the
menu. I tried with the "list" option but only the first mdcrd was opened.

When you run MD Movie and the dialog comes up where you specify the prmtop/trajectory files, you can use the "Add..." button to add as many trajectory files as needed. I think this means you "give it at the beginning" rather than "subsequently from the menu" in your terminology.

You can also just list the files in a "metafile" for the command line. For instance, this file works for me:

amber

leap.top

md01.crd

md02.crd

md03.crd

md04.crd

md05.crd

md06.crd

Note that there _still_ seems to be something funky with Amber compressed trajectories, so don't use them for now but I should have things fixed in a day or so with that.

--Eric