Hi pymol-users list,
In case anyone else runs into this problem, I've been able to use a
work-around to avoid this glitch. Paul Emsley suggested I export a finer
sampled map from coot to avoid needing the map_double command in pymol.
This work-around works for me, and while the file size for the map is
enormous, it removes the artifact from my images.
For the curious, images of the same map sampled at 2.5 and 5.0 are linked
below, along with the default-sampled map and its map_doubled children:
2.5: http://imgur.com/WpBDNvw
5.0: http://imgur.com/Ryw3X0T
Default (1.5 sampled) map: http://imgur.com/i46YH6r
Doubled once: http://imgur.com/Vy8oJfx
Doubled twice: http://imgur.com/q3gO0cI
Cheers,
Shane Caldwell
McGill University
On Thu, Dec 11, 2014 at 3:08 PM, Shane Caldwell <shane.caldwel...@gmail.com>
wrote:
> Hi Pymol Users,
>
> I have a problem drawing maps, and can't seem to find the solution online,
> so thought I'd ask here.
>
> 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
>
> Thanks!
>
> Shane Caldwell
> McGill University
>
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