On 18/01/15 18:29, Kenneth A. Satyshur wrote:
Coot is our best program there ever was for fitting electron density. It is very simple to use and easy to teach. But sometimes improvements are made that seem to just slow things down. Having used 0.7.1 for a long time, i noticed that rotation and scaling of density is very quick, but translations are much slower (cntrl left mouse). Now in 0.8.1, translations have become impossibly slow. They freeze the whole graphics system for as long as 10 seconds. It is recalculating a map, and this can be seen using top to display the cpu usage.
Let me encourage you to read section 9.12 of the manual. Here's the link: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration
Also, we are now given a spherical density, which is annoying,
You are not the first disapprove of the change - others have been somewhat less forthright, however.
really, since cell edges are not spherical and its hard to examine 3D space in a bubble. But there must be a way of speeding up the recalculation of the map during translation. I have a dual quad core with 15 idle cores while coot recalculates its new map in one core. Maybe multi core is the way to go. I hope this can be fixed.
I believe that there have been advances in rendering 3D scalar data (such as medical imaging) using the GPU. It would be nice if an implementation of such were ported to Coot
https://github.com/smistad/GPU-Marching-Cubes
Otherwise I will stick with the 0.7 version that makes a cuboid map. I really enjoy the rapid examination of density that coot provides especially in 3D.
I'll consider adding a "display-density-as-the-old-box" configuration flag.
thanks to the Coot team.
You're welcome. Paul.
