5365 atoms? Given average atom counts in protonated protein residues that means your ligand came in close contact with ~340 residues over the course of the trajectory -- so it's wandering all over the place. I can see why you want to use cluster analysis. Oh well, I guess we're stuck until I have time to coordinate with Conrad and integrate his clustering code with MD Movie. --Eric On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote:
Eric: I followed previous route from combined mdcrd from ptraj.
Removed remaining water.
select ligand z<2.5
as Chimera command; (this was the minimum, selecting 244 atoms, 118 of which for the ligand; with z<2.0 the ligand only is selected)
On playing the pdb (saved for selected atoms only) (with LOOP deselected) the atom selection increased, reaching 5365 atoms at the last (549) frame. In another run, with z<4.0 the course of atom selection was similar, reaching 5993 atoms at frame 549.
This huge number of atoms proved problematic for opening pdb. For the z<2.5 case I left the computer on for 4h and half, with python occupying 98% of the available MEM (nearly 1GB). I had to kill gnome to recover command.
May be with much more MEM it will work, though I can't check that now.
I did not try to combine the trajectories with Chimera as I have no indication that those from ptraj are faulty. The pdb files for both z<2.5 and z<4.0 open in vmd.
francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
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
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