-------- 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
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