----- Ursprüngliche Mail -----
> Von: [email protected]
> An: [email protected]
> Gesendet: Mittwoch, 24. November 2010 16:26:39
> Betreff: Re: [Jmol-users] obj surface files exported from pymol
> On Wed, November 24, 2010 10:17 am, Alexander Rose wrote:
> > Manipulating the pdb file before creating the surface with PyMOL
> > does not
> > work because the PyMOL obj has no relation to the pdb coordinates.
>
> Isn't this something pymol should do? Maybe suggest a
> bug-fix/enhancement
> on the pymol list?
>
i did and got the following answer:
"Thanks for writing. I don't consider this a bug because most people
use the exported geometry with respect to the center of mass of the
structure, not the origin on the coordinate axes. I will, however,
try to add a setting for future versions of PyMOL to allow for both
local coordinates and global coordinates."
and my question
"Macintosh: MacPyMOL-v1.3r1
when issuing save surface.obj a obj file is written that is centered at {0 0
0} and rotated as in the current view. This makes it hard to use the
exported surface in other programs to i.e. compare the surface algorithms.
Do you consider this a bug? Are there any options to change this behavior?
Is it intended?"
anyway with Bob suggestion
load xxxx.pdb
isosurface OBJ xxxxx.obj offset @{ {*}.xyz }
jmol can "use the exported geometry with respect to the center of mass of the
structure, not the origin on the coordinate axes"
Alex
> Rich
>
>
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