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

[Tom Goddard]

Hi Alexis,

  The pseudobond reader could be improved to set the dashes.  But all the pseudobonds in a pseudobond model must have the same number of dashes.  So your example of setting 2 different dashes values in the file won't work.

	Tom


> On Mar 10, 2020, at 9:51 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> 
> Well, it's good to know I'm the only one who sometimes fails to RTFM :)
> 
> While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this:
> 
> ; pseudo bonds for figure
> ; radius = 0.05
> ; dashes = 3
> #1/L at H42 #1/B:940 at OE1 rgba(12,56,100,0.2)
> #1/L at O11 #1/A:840 at HH dodgerblue
> #1/B:940 at HE21 #1/B:887 at OG dodgerblue
> ; dashes = 8
> #10841 #1/A:840 at CD2 yellow
> #10884 #1/A:840 at CE1 yellow
> #10840 #1/B:940 at HE22 yellow
> #10001 #1/B:947 at CZ yellow
> #10002 #1/A:841 at CZ yellow
> 
> On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
> 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 <mailto: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 <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 <mailto: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 <mailto: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 <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>>
> > 
> > 
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