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

Tue Mar 10 11:08:01 PDT 2020

Hi Alexis,

  I added dashes, color and halfbond variables to the ChimeraX pseudobond file format, example below.  The radius, color and halfbond settings can be set multiple times in the file, applying to the lines below them, while dashes is a global setting.

	Tom

; radius = 0.075
; color = orange
; halfbond = false
; dashes = 13
/D:38 at OD2	/C:436 at OH	
/D:38 at OD1	/C:482 at CA	
; color = yellow
/D:38 at OD1	/C:436 at OH	

> On Mar 10, 2020, at 10:16 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> 
> Thanks both. I'll just do separate files as needed and set the dashes via style. 
> 
> On Tue, Mar 10, 2020 at 10:14 AM Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
> 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 <mailto: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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