[chimerax-users] pseudobond between atom and center of a ring

[Elaine Meng]

Hi Alexis, 
I can reproduce the problem with reading the pb file transparency using a color specification of the form:

/a:1 at c3' /a:1 at n3 rgba(20,90,90,70)

However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:

/a:1 at c3' /a:1 at n3  20,90,90,70
- OR -
/a:1 at c3' /a:1 at n3  #00ced155

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>

Those atoms are in PDB 1bna, for example.  Tested in current daily build
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> 
> Thanks Elaine!
> 
> Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
> 
> Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
> 
> Thanks again for the help. 
> 
> Cheers,
> Alexis
> 
> On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Here is the more detailed description of pseudobond file format:
> 
> <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>