[chimerax-users] C-alphas rendered as dots

[Pranav Shah]

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 at 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 at 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 at 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 at 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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> >>>
> >>
> >
>