Hi Marcelo - No I don't believe so. In PyMOL, a CGO `CONE` is a fixed-length list of floats. You can see in the cgo.py source <https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py#L65> that `cgo.CONE` itself is actually a float, too (specifically, 27.0). My understanding is that under-the-hood the parser is doing something like:
1. Look at the list of floats passed to `cmd.load_cgo()` and read the first one as an instruction; 2. Determine how many more values to expect from that instruction (e.g. for `CONE` it would expect 16 additional floats); 3. Read those values and use them to create the geometry; 4. If there are any values left in the list, treat the next float as a completely separate instruction, and repeat this process until there are no values left. In order to add alpha to a color channel (which I'm not even sure is compatible with the way PyMOL handles colors—though I'd leave that question to one of the developers), one would have to add an additional instruction keyword in cgo.py with a different expected set length of float arguments, then implement how to translate that instruction into geometry in the underlying C++. Of course if that's something you're really interested in doing, you could certainly take a crack at implementing it in Open Source PyMOL and submit a pull request. :) Hope that helps. Cheers, Jared On Sun, Feb 13, 2022 at 9:49 PM Marcelo Depólo Polêto < marcelodep...@gmail.com> wrote: > Thank you Jared, > > Yes, I have been using *set cgo_transparency*, but is there a way of > embedding alpha in the CONE object definition? Since I have been using > color1='blue' and color2='red', can I just append an alpha float to the > color lists? > > Best regards, > -- > Marcelo > > Em dom., 13 de fev. de 2022 às 21:42, Jared Sampson < > jared.samp...@columbia.edu> escreveu: > >> I forgot to add that the transparency can be handled by e.g. >> >> set cgo_transparency, 0.5, my_cgo_object >> >> Cheers, >> Jared >> >> On Sun, Feb 13, 2022 at 9:38 PM Jared Sampson <jared.samp...@columbia.edu> >> wrote: >> >>> Hi Marcelo - >>> >>> Looks like you have the right format for `CONE`. This should really be >>> in the Wiki...and apparently is not. I've just made a couple of pages, >>> others can of course feel free to elaborate: >>> >>> https://pymolwiki.org/index.php/CGO_Shapes >>> https://pymolwiki.org/index.php/Load_CGO >>> >>> You may also find it useful to look at the Open Source PyMOL source >>> code, perhaps starting with: >>> >>> https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py >>> >>> Hope that helps. >>> >>> Cheers, >>> Jared >>> >>> >>> On Sat, Feb 12, 2022 at 10:51 PM Marcelo Depólo Polêto < >>> marcelodep...@gmail.com> wrote: >>> >>>> Hi all, >>>> >>>> I am building a CGO object of a cone and I want to embed a transparency >>>> value to it. So far I managed to create the cone with the line below: >>>> >>>> *obj = [cgo.CONE] + begin + end + [radius_begin, radius_end] + color1 + >>>> color2 + [1.0, 1.0]* >>>> >>>> Could someone provide more information on how the CGO objects are >>>> structured (which values are expected and their formats)? >>>> >>>> Best regards, >>>> -- >>>> *Marcelo Depólo Polêto, Ph.D.* >>>> Postdoctoral Associate >>>> Office: 106B Engel Hall >>>> Department of Biochemistry >>>> Virginia Tech >>>> 340 West Campus Dr. >>>> Blacksburg, VA 24061 >>>> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>: >>>> he/him/his >>>> _______________________________________________ >>>> PyMOL-users mailing list >>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>>> Unsubscribe: >>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >>> >>> > > -- > -- > *Marcelo Depólo Polêto, Ph.D.* > Postdoctoral Associate > Office: 106B Engel Hall > Department of Biochemistry > Virginia Tech > 340 West Campus Dr. > Blacksburg, VA 24061 > gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>: > he/him/his >
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