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.
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