On Mar 10, 2020, at 10:16 AM, Alexis Rohou <a.rohou@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@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@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@H42 #1/B:940@OE1 rgba(12,56,100,0.2)
#1/L@O11 #1/A:840@HH dodgerblue
#1/B:940@HE21 #1/B:887@OG dodgerblue
; dashes = 8
#10841 #1/A:840@CD2 yellow
#10884 #1/A:840@CE1 yellow
#10840 #1/B:940@HE22 yellow
#10001 #1/B:947@CZ yellow
#10002 #1/A:841@CZ yellow

On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng@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@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@c3' /a:1@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@c3' /a:1@n3  20,90,90,70
> - OR -
> /a:1@c3' /a:1@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@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@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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