[phenixbb] Intensity-Weighted Reciprocal Lattice

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Wed Aug 3 02:46:48 PDT 2011

Hi Nat - pretty neat!  I had a look yesterday;  no detailed comments, 
but I found it very hard to make sense of anything, and eventually 
figured out why:  the lattice flashes on-and-off during rotation.  So 
the eye cannot hold onto anything, so it's almost completely pointless.

That was with spheres drawn, on CentOS5 (or something).

I didn't immediately find pan, zoom and slab functions;  but if they're 
not on the mouse, the way coot and pymol have them, it probably won't be 
too useful either.

Hope that helps!

On 22/07/2011 02:50, Nathaniel Echols wrote:
> On Thu, Jul 21, 2011 at 6:36 PM, Michael Thompson<miket at chem.ucla.edu>  wrote:
>> I know that there are several programs out there that can generate sections (i.e. 0,k,l) of the reciprocal lattice, such as LABELIT and xrayplot. Are there any other options for doing this, perhaps within ccp4 and/or phenix? I once saw someone give a presentation and they had a little video that showed a three dimensional section of the reciprocal lattice rocking back and forth, which was really cool. I liked this because I felt like it gave a much more holistic representation as opposed to viewing a bunch of individual sections. I don't know if there is an easy way to do this, or if this person somehow managed to create this 3D depiction from a series of sections.
> "hklview" is the classic ccp4 program for viewing 2D slices, but there
> is a much more modern version on CCP4's "prerelease software" site
> called "ViewHKL".  For some reason they decided not to release it with
> ccp4 6.2, but it's very nice.
> For a 3D view of reciprocal space, try phenix.data_viewer, also a
> button in the main GUI.  (It does 2D display too - this may be more
> useful than 3D for visualizing some pathologies like translational
> NCS.)  It's still under development - you'll need a recent nightly
> build.  There's no animation support, but now that you've mentioned
> it...
> -Nat
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