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

[Alexis Rohou]

Wow, that's awesome, thanks! I'll install the daily build tomorrow to try
it out.

On Tue, Mar 10, 2020 at 11:08 AM Tom Goddard <goddard at sonic.net> wrote:

> 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> 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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