[Chimera-users] Chimera-users Digest, Vol 42, Issue 2

[Jonathan Hilmer]

Pu Qian,

Although resources-intensive, I find it useful to have multiple,
identical, overlapping copies of the same density set.  It allows
complex 'removal' of sections in the final image by the combination of
multiple clipping planes.  For example, the three planes with
definitions of [1,0,0], [0,1,0], and [0,0,1] all with an origin at the
center of your data will cut away 1/8 of a spherical region, if you
have three copies of the density loaded.  This also makes it easy to
animate the cutout.  The alternative is to use the volume eraser
(http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html),
which works, but I've found it less useful for movies.  When working
with large data sets and this method, use cropped density sets to
minimize unnecessary resource usage.

Jonathan


> > To whom it may concern,
> >
> > I'm a new user of Chimera. It is a very good software!
> >
> > Here, I would like to ask you a few questions? To show inside of
> > protein
> > (3d model),I need to cut it into half (sometime, maybe only part,
> > for example,
> > 1/4 etc.). Just like an apple, if I want to show its core, I need
> > to cut the
> > apple into two parts from its middle. Does Chimera has such
> > function? (I think
> > it has.) My 3d data comes from electron microscopy single particle
> > analysis
> > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so,
> > which type of
> > 3d data I should produce for Chimera? It would be a great
> > appreciated if you
> > could reply me in your convenience. Hope it will not bother you too
> > much.
> >
> > Sincerely yours,
> >
> >
> > Pu Qian
> >
> > Dr. Pu Qian
> > Department of Molecular Biology
> > The University of Sheffield
> > Firth Court, Western Bank
> > Sheffield, S10 2TN
> > UK