-------- Original Message -------- From: "Kenneth A. Satyshur" Date: Jan 22, 2015 12:45:49 PM Subject: Re: [ccp4bb] coot 0.8.1 freezes my graphics To: Paul Emsley
> Thanks for the hints. I have tried some of these. Here is why I think it is > graphics (coding). > Turn off the density and turn off the molecule and leave just the 'box'. > Rotations happen in real time, > but translations do not. It is equally slow even without asking for an image > to be displayed. I > use molecular graphics extensively and there should be no difference in > moving inside a space as > moving thru a space. In a graphics run program, like Sybyl from Tripos, all > work is done by the > graphics engines. Rotations and translations are equally fast. In a > non-graphics engine program like > pymol, the image is recalculated in the processor in real time, thus slowing > down the response. I can run > sybyl on a computer on one end of campus and display it on the other end > (over a mile away, this is how I teach) > and it will rotate and translate in real time. Sybyl sends graphics info to > the graphics card on my > display machine where they are rendered. I cannot do the same with pymol. > > Nevertheless.... I will always use coot! It is still the best. > > kas > > > On 01/19/15, Paul Emsley > wrote: > > 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. > > -- > Kenneth A. Satyshur, M.S.,Ph.D. > Senior Scientist > University of Wisconsin > Madison, Wisconsin 53706 > 608-215-5207 -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207
<<attachment: satyshur.vcf>>
<<attachment: satyshur.vcf>>
