Hi Tom,
I have filed a bug report, with a description as well as the PDB file
that I was using when I chanced upon this observation.
Looking forward to hearing from you.
Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK
On Mon, Aug 2, 2021 at 7:08 PM Tom Goddard <
goddard@sonic.net> wrote:
And did using simple lighting fix the slow rigid-body fitting? If not, is the slowness when you are trying to move one model with the mouse. If so, what graphics card are you using? ChimeraX should easily move a million atoms pretty smoothly with a mid-range graphics card. If you want to further discuss this probably good to use ChimeraX menu Help / Report a Bug so we get you computer system info.
Tom
On Aug 2, 2021, at 10:58 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Tom,
I was aware of this and had therefore done exactly what you suggested! :)
Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK
On Mon, Aug 2, 2021 at 6:36 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav,
The main think that makes ChimeraX sluggish when moving individual models with the mouse for doing rigid-body fitting is full or soft lighting modes that cast ambient shadows. If you switch to simple lighting using the Home toolbar icon or command "light simple" then graphics updating will be many times faster. The reason for the slow graphics with ambient shadows is that it is recomputing shadows from 64 different directions when you move one model relative to the other because the models cast shadows on each other. I am thinking of having ChimeraX issue warning when graphics becomes slow due to continuous updating of ambient shadows so it will be more obvious how you fix it.
Tom
On Aug 2, 2021, at 7:15 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am working with a huge model (and a correspondingly huge map), which
makes the handling on my GPU accelerated desktop an agonisingly
frustrating experience. In order to speed up simple (rigid-body)
fitting of the map and model, I decided to use the -C-alpha trace of
the pdb. However, the pdb gets rendered as a bunch of disconnected
dots whereas the same pdb in Chimera is rendered correctly with all
things. Is this a normal behaviour for ChimeraX? I could use Chimera,
but I prefer the way ChiemraX handles large maps as compared to
Chimera. In the absence of a quick fix, would there be a way to
increase the size of the atoms?
Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK
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