Quick follow-up: I just learned from Jarrett Johnson that it is possible to add alpha to CGO objects on a per-shape basis. Just prepend `[cgo.ALPHA, 0.5]` (substituting your desired alpha value, of course) before the CONE (or other) shape. This alpha value will be used for all subsequent shapes until you set another `cgo.ALPHA` value by the same method.
Hope that helps. Cheers, Jared On Mon, Feb 14, 2022 at 10:04 AM Jared Sampson <jared.samp...@columbia.edu> wrote: > 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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