[PyMOL] RE: NOTICE: mail delivery status

[Warren D. <wa...@de...>]

Now this has got to be the funniest bounce I've received to date as
administrator of the PyMOL users list:

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> pos...@na...
> Sent: Sunday, November 20, 2005 7:40 PM
> To: pym...@li...
> Subject: NOTICE: mail delivery status
>=20
> Mail Delivery Failure
>=20
> A message sent to <name-deleted-to-protect-the-innocent> was not=20
> delivered for the following reason:
>=20
> 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? =20

> multiple molecules (e.g. dimer)? Amber should not 'cut' your=20
> molecule into pieces, imaging can only separate molecules in=20

Check.  Stripping? =20

> a dimer, trimer or such.  Also, was your system solvated? Did=20
> you strip water before visualizing in PyMOL? There may be an=20

Gotcha.  Breaking? =20

> There may be an=20
> issue with your trajectory containing box information which=20
> might break a correspondence of trajectory coordinates and=20
> topology.=20

No doubt.  Messing things up?

> > I have a problem with viewing AMBER trajectory files,=20
> specifically, =20
> > the topology appears messed up.

Right on.  Dismembering?

> > When I load the trajectory into the =20
> > topology object, the structure shows up dismembered into=20
> eight pieces =20
> > on the vertices of a cube.=20
 =20
Excellent. =20

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. =20

PyMOL-users email censored due to violence!  What a laugh.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Viktor Hornak
> Sent: Sunday, November 20, 2005 7:40 PM
> To: pym...@li...
> Subject: Re: [PyMOL] problem with amber trajectory]
>=20
> Dmitry,
>=20
> is your system a single molecule or is it composed of=20
> multiple molecules (e.g. dimer)? Amber should not 'cut' your=20
> molecule into pieces, imaging can only separate molecules in=20
> a dimer, trimer or such.  Also, was your system solvated? Did=20
> you strip water before visualizing in PyMOL? There may be an=20
> issue with your trajectory containing box information which=20
> might break a correspondence of trajectory coordinates and=20
> topology. To test this, see if the first frame of your=20
> trajectory looks ok but all others don't. ptraj is a good=20
> program to do various manipulations with your trajectory as=20
> Warren suggested.
>=20
> Cheers,
> -Viktor
>=20
>=20
> Dmitry Kondrashov wrote:
>=20
> > Hi,
> >
> > I have a prloblem with viewing AMBER trajectory files,=20
> specifically, =20
> > the topology appears messed up. When I load the trajectory=20
> into the =20
> > topology object, the structure shows up dismembered into=20
> eight pieces =20
> > on the vertices of a cude. I should note that I can load an AMBER =20
> > coordinate file into the same topology with no problem, and=20
> that the =20
> > trajectory displays just fine in VMD.
> > I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in =20
> > 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