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

[Alexis Rohou]

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> 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> 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> 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> 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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