Re: [PyMOL] MacPyMOL Knowledge of Opened Structures

[Jason V. <jas...@sc...>]

Hi Sean,

Sorry to hear you're having problems.

> 1) Load A.pdb into MacPyMOL via "pymol A.pdb"
> 2) Load a CHARMM simulation trajectory into object "A" via "load A.dcd, A"
>
> 3) Load a completely different structure (must have different number of
> atoms than A.pdb), B.pdb, into a separate/new instance/window of MacPyMOL
> via "pymol B.pdb"
> 4) Load a CHARMM simulation trajectory into object "B" via "load B.dcd, B"
>
> Loading of this second trajectory complains with the following error:
>
> ObjectMolecule: plugin 'dcd' cannot open file because the number of atoms in
> the object (4551) did not equal the number of atoms in the 'dcd' (5889)
> file.

I wrote this error message. PyMOL counts the atoms in the object and
makes sure each frame of the trajectory has an equivalent number. This
stops PyMOLers from accidentally working with incorrectly paired data
-- which happened quite a bit.

> I should mention that in the real example, "A.pdb" and "B.pdb" actually have
> the same name but are located in different directories (in case it matters).

Seeing this makes me think of two possibilities. First, you possibly
made a simple mistake on disk and B.pdb and B.dcd don't actually
match. Do these _exact_ files using the exact same commands work the
same in Linux? (Can you md5sum the files to check?) Second, if PyMOL
is sharing data then, because they have the same file name, you'll
have to rename one to something else, like "A2".

Let us know.

Cheers,

-- Jason



>
> In this error, the number "5889" corresponds to the number of atoms in A.pdb
> while "4551" corresponds to the number of atoms in B.pdb.  Again, these are
> two separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb into
> the same window).  Somehow, the first instance of PyMOL sees what is
> happening in the other.
>
> I should mention that in the real example, "A.pdb" and "B.pdb" actually have
> the same name but are located in different directories (in case it matters).
>
> On a non-Mac machine, these commands are fine.  As an "experienced" PyMOL
> user, it was quite embarrassing when a set of commands/steps that worked on
> a Linux workstation does not work on a Mac (especially when I was trying to
> show the simulations to a VMD user).  I'm fairly new to Macs so maybe
> there's something that I need to do?
>
> Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't seem
> to run "hide all" and "show cartoon" from my .pymolrc.
>
> Any help/suggestions would be greatly appreciated!
>
> Sean
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120