Now this has got to be the funniest bounce I've received to date as administrator of the PyMOL users list:
> -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of > [email protected] > Sent: Sunday, November 20, 2005 7:40 PM > To: [email protected] > Subject: NOTICE: mail delivery status > > Mail Delivery Failure > > A message sent to <name-deleted-to-protect-the-innocent> was not > delivered for the following reason: > > Language in the message triggered the following rule(s): > Violence (English) What? Violence on the PyMOL Mailing List? Hmm, let's see... What about cutting? > multiple molecules (e.g. dimer)? Amber should not 'cut' your > molecule into pieces, imaging can only separate molecules in Check. Stripping? > a dimer, trimer or such. Also, was your system solvated? Did > you strip water before visualizing in PyMOL? There may be an Gotcha. Breaking? > There may be an > issue with your trajectory containing box information which > might break a correspondence of trajectory coordinates and > topology. No doubt. Messing things up? > > I have a problem with viewing AMBER trajectory files, > specifically, > > the topology appears messed up. Right on. Dismembering? > > When I load the trajectory into the > > topology object, the structure shows up dismembered into > eight pieces > > on the vertices of a cube. Excellent. Congratulations Victor and Dmitry, you have won the Abdul Alhazred award for 2005. Who needs a Necronomicon, when you've got the PyMOL mailing list? Lovecraft would be proud. PyMOL-users email censored due to violence! What a laugh. Cheers, Warren > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of > Viktor Hornak > Sent: Sunday, November 20, 2005 7:40 PM > To: [email protected] > Subject: Re: [PyMOL] problem with amber trajectory] > > Dmitry, > > is your system a single molecule or is it composed of > multiple molecules (e.g. dimer)? Amber should not 'cut' your > molecule into pieces, imaging can only separate molecules in > a dimer, trimer or such. Also, was your system solvated? Did > you strip water before visualizing in PyMOL? There may be an > issue with your trajectory containing box information which > might break a correspondence of trajectory coordinates and > topology. To test this, see if the first frame of your > trajectory looks ok but all others don't. ptraj is a good > program to do various manipulations with your trajectory as > Warren suggested. > > Cheers, > -Viktor > > > Dmitry Kondrashov wrote: > > > Hi, > > > > I have a prloblem with viewing AMBER trajectory files, > specifically, > > the topology appears messed up. When I load the trajectory > into the > > topology object, the structure shows up dismembered into > eight pieces > > on the vertices of a cude. I should note that I can load an AMBER > > coordinate file into the same topology with no problem, and > that the > > trajectory displays just fine in VMD. > > I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in > > loading the trajectory, here's the last few lines: > > > > ObjectMolecule: read set 757 into state 757... > > ObjectMolecule: read set 758 into state 758... > > CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w". > > CmdLoadTraj: 758 total states in the object. > > > > I appreciate your help, > > Dmitry
