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