Re: [ccp4bb] Off-topic - PyMol map sampling at unit cell boundary
Hi all, To follow up on my question from last week, Dr. Emsley's work-around worked great for me. Increase map sampling in coot, export, and then proceed in pymol without using the map_double command. I end up with gigantic map file sizes (~160MB), and it's more work to make all my maps this way, but it gets me past the problem. 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 Fri, Jan 9, 2015 at 4:57 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: 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.
Re: [ccp4bb] Off-topic - PyMol map sampling at unit cell boundary
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.
[ccp4bb] Off-topic - PyMol map sampling at unit cell boundary
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 Thanks for your indulgence! Shane Caldwell McGill University
