[PyMOL] Ray tracing transparent sticks

Hello! I have been trying to ray trace stick representations with transparency (i.e. stick_transparency = 0.5). Although surface transparency is visible in ray tracing, transparent sticks always appear opaque in the rendered image. Is there a way to resolve this? Note that in OpenGL, stick tra

[PyMOL] Open source v2.3.3

Hello, I am using open-source pymol v2.3.0. However I have come across a bug when trying to ray trace transparent sticks, where transparency is not rendered at all. In a previous mail of mine, I was told that this issue had been fixed in version 2.3.3. This version is not available in GitHub to

[PyMOL] Can't install latest version on Mac

Hello, I have been trying to install the latest version of Pymol from GitHub on Catalina, following the compilation instructions in INSTALL. The process fails all the times, with lots of compilation warnings and errors. I have also used Homebrew, but the respective formula points to version 2.3.

[PyMOL] Importing Pymol as library

Good afternoon, I am using pymol as a python library for a pipeline, in which I just use some fitting functions (no GUI). Is there a way to suppress the warning ‘PyMOL not running, entering library mode (experimental)’? Thanks, Yannis ___ PyMOL-users

[PyMOL] Custom selection operators

Hello, Is there any way to define a custom selection operator in a script? E.g. select all atoms with complex properties A, B, and C. Otherwise, what is the proper way of appending atoms to a selection in scripting? Thank you, Yannis ___ PyMOL-

[PyMOL] Custom selection operators

Hello, Is there any way to define a custom selection operator in a script? E.g. select all atoms with complex properties A, B, and C. Otherwise, what is the proper way of appending atoms to a selection in scripting? Thank you, Yannis ___ PyMOL-u

[PyMOL] ImportError when launching open-source pymol

Hello, Anyone any idea how to tackle this error when launching pymol after compiling from source? ImportError: /hps/software/users/xx/xx/miniconda3/envs/py3/lib/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so: undefined symbol: _Z15MapSetupExpressP7MapType Trial version work

[PyMOL] Default altloc selection

Hello, Is there a way to set a default altloc to be selected, if the residue/atom is disordered? I can do this manually with a notation like ‘select foo, obj//chain/resid/atom and alt A’ but if the residue/atom is not disordered, the selection will be empty (I call this through a script for a s