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

[Elaine Meng]

Oops, didn't read my own documentation carefully enough!

When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do.  The transparency number has to be in the range 0-1.

So you would need something like the following, which also works.  Tested in daily build and in release 0.92.

rgba(20%,90%,90%,0.7)

Sorry for the mistake -- I normally use the simpler form:  20,90,90,70
Elaine

> On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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>
> 
> 
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