On 09/01/15 21:08, Shane Caldwell wrote:
Hi ccp4bb,
Apologies for a cross-post. I previously asked this question on the
pymol-users mailing list, but I thought I'd ask here as well, in case
someone who doesn't follow that bb might have run into my problem
rendering maps in PyMol. I'm starting to think it's a non-trival
problem to solve.
I'm drawing a mesh based on a ccp4 map exported from coot. To get
finer sampling, I use the map_double command (twice sequentially, but
the problem is visible after the first). Doubling the map introduces a
discontinuity. The second doubling introduces a gap, but even even the
first has a visible distortion. (see linked images below)
This discontinuity lines up with the unit cell boundary, so it has
something to do with sampling at the unit cell edge (the cell boundary
is faintly visible in the background of the linked images). Not sure
if there's a simple fix I'm overlooking or if it's a fundamental
limitation of the sampling algorithm. Any help you can provide would
be great!
I've linked images of the same map at all 3 samplings below:
Parent map: http://imgur.com/i46YH6r
Doubled once: http://imgur.com/Vy8oJfx
Doubled twice: http://imgur.com/q3gO0cI
That's amusing. Looks like a pymol bug (but of course, given the source
of this comment, you should take that with a pinch of salt).
As a work-around, I'd advise that you turn up the map sampling rate to
2.8 or so in Coot (before you read in your mtz file and subsequently
export the map (fragment)) - then you won't need pymol map doubling.
Paul.
