Volumes Don't Render in command-line only mode

[kmdalton]

Describe the bug

If I run pymol example.pml in the attached example, the output .png file shows the expected electron density volume. However, when I run pymol -c example.pml the volume doesn't appear in the .png file.

To Reproduce

1. Download example.zip
2. unzip example.zip
3. cd example
4. pymol -c example.pml

Expected behavior

1ubq.png produced by pymol example.pml works as expected:

1ubq.png produced by pymol -c example.pml is missing the electron density volume

Environment

• PyMOL Version: PyMOL 3.1.0 Open-Source, 2025-09-04
• Installed from conda-forge using conda install -c conda-forge pymol-open-source
• MacOS 15.6.1 (24G90)
• conda list:

# packages in environment at /Users/kmdalton/opt/anaconda/envs/pymol-os:
#
# Name                    Version                   Build  Channel
blosc                     1.21.6               h7dd00d9_1    conda-forge
bzip2                     1.0.8                hd037594_8    conda-forge
c-ares                    1.34.5               h5505292_0    conda-forge
ca-certificates           2025.10.5            hbd8a1cb_0    conda-forge
contourpy                 1.3.3                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
cyrus-sasl                2.1.28               ha1cbb27_0    conda-forge
fonttools                 4.60.1                   pypi_0    pypi
freetype                  2.14.1               hce30654_0    conda-forge
gemmi                     0.7.3                    pypi_0    pypi
gemmi-program             0.7.3                    pypi_0    pypi
glew                      2.1.0                h9f76cd9_2    conda-forge
glib                      2.86.0               h52a91e1_0    conda-forge
glib-tools                2.86.0               hb9d6e3a_0    conda-forge
glm                       1.0.1                h6597b73_0    conda-forge
gst-plugins-base          1.24.11              h3c5c1d0_0    conda-forge
gstreamer                 1.24.11              hfe24232_0    conda-forge
hdf4                      4.2.15               h2ee6834_7    conda-forge
hdf5                      1.14.6          nompi_he65715a_103    conda-forge
icu                       75.1                 hfee45f7_0    conda-forge
kiwisolver                1.4.9                    pypi_0    pypi
krb5                      1.21.3               h237132a_0    conda-forge
libaec                    1.1.4                h51d1e36_0    conda-forge
libblas                   3.9.0           36_h51639a9_openblas    conda-forge
libcblas                  3.9.0           36_hb0561ab_openblas    conda-forge
libclang-cpp17            17.0.6          default_hf90f093_8    conda-forge
libclang13                21.1.0          default_h6e8f826_1    conda-forge
libcurl                   8.14.1               h73640d1_0    conda-forge
libcxx                    21.1.2               hf598326_0    conda-forge
libedit                   3.1.20250104    pl5321hafb1f1b_0    conda-forge
libev                     4.33                 h93a5062_2    conda-forge
libexpat                  2.7.1                hec049ff_0    conda-forge
libffi                    3.4.6                h1da3d7d_1    conda-forge
libfreetype               2.14.1               hce30654_0    conda-forge
libfreetype6              2.14.1               h6da58f4_0    conda-forge
libgfortran               15.2.0               hfcf01ff_1    conda-forge
libgfortran5              15.2.0               h742603c_1    conda-forge
libglib                   2.86.0               h1bb475b_0    conda-forge
libiconv                  1.18                 h23cfdf5_2    conda-forge
libintl                   0.25.1               h493aca8_0    conda-forge
libintl-devel             0.25.1               h493aca8_0    conda-forge
libjpeg-turbo             3.1.0                h5505292_0    conda-forge
liblapack                 3.9.0           36_hd9741b5_openblas    conda-forge
libllvm17                 17.0.6               hc4b4ae8_3    conda-forge
libllvm21                 21.1.0               h846d351_0    conda-forge
liblzma                   5.8.1                h39f12f2_2    conda-forge
libnetcdf                 4.9.3           nompi_h6808abe_102    conda-forge
libnghttp2                1.67.0               hc438710_0    conda-forge
libntlm                   1.8                  h5505292_0    conda-forge
libogg                    1.3.5                h48c0fde_1    conda-forge
libopenblas               0.3.30          openmp_h60d53f8_2    conda-forge
libopus                   1.5.2                h48c0fde_0    conda-forge
libpng                    1.6.50               h280e0eb_1    conda-forge
libpq                     17.6                 h31f7a3a_2    conda-forge
libsqlite                 3.50.4               h4237e3c_0    conda-forge
libssh2                   1.11.1               h1590b86_0    conda-forge
libvorbis                 1.3.7                h81086ad_2    conda-forge
libxcb                    1.17.0               hdb1d25a_0    conda-forge
libxml2                   2.13.8               h4a9ca0c_1    conda-forge
libzip                    1.11.2               h1336266_0    conda-forge
libzlib                   1.3.1                h8359307_2    conda-forge
llvm-openmp               21.1.2               h4a912ad_3    conda-forge
lz4-c                     1.10.0               h286801f_1    conda-forge
matplotlib                3.10.6                   pypi_0    pypi
ncurses                   6.5                  h5e97a16_3    conda-forge
nspr                      4.37                 h31e89c2_0    conda-forge
nss                       3.117                h1c710a3_0    conda-forge
numpy                     2.3.3           py312h85ea64e_0    conda-forge
openldap                  2.6.10               hbe55e7a_0    conda-forge
openssl                   3.5.4                h5503f6c_0    conda-forge
packaging                 25.0               pyh29332c3_1    conda-forge
pcre2                     10.46                h7125dd6_0    conda-forge
pillow                    11.3.0                   pypi_0    pypi
pip                       25.2               pyh8b19718_0    conda-forge
ply                       3.11               pyhd8ed1ab_3    conda-forge
pmw                       2.0.1           py312h81bd7bf_1008    conda-forge
pthread-stubs             0.4               hd74edd7_1002    conda-forge
pymol-open-source         3.1.0           py312h5cdc5c8_1    conda-forge
pyparsing                 3.2.5                    pypi_0    pypi
pyqt                      5.15.11         py312h6612b97_2    conda-forge
pyqt5-sip                 12.17.0         py312h455b684_2    conda-forge
python                    3.12.11         hc22306f_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python_abi                3.12                    8_cp312    conda-forge
qt-main                   5.15.15              hac936aa_5    conda-forge
readline                  8.2                  h1d1bf99_2    conda-forge
setuptools                80.9.0             pyhff2d567_0    conda-forge
sip                       6.13.0          py312h455b684_0    conda-forge
six                       1.17.0                   pypi_0    pypi
snappy                    1.2.2                hd121638_0    conda-forge
tk                        8.6.13               h892fb3f_2    conda-forge
toml                      0.10.2             pyhd8ed1ab_1    conda-forge
tomli                     2.2.1              pyhe01879c_2    conda-forge
tzdata                    2025b                h78e105d_0    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
xorg-libx11               1.8.12               h6a5fb8c_0    conda-forge
xorg-libxau               1.0.12               h5505292_0    conda-forge
xorg-libxdmcp             1.1.5                hd74edd7_0    conda-forge
xorg-libxfixes            6.0.2                hc919400_0    conda-forge
zlib                      1.3.1                h8359307_2    conda-forge
zstd                      1.5.7                h6491c7d_2    conda-forge

I also see this problem in the incentive PyMOL,

• PyMOL 3.1.4.1 Incentive Product (fd4543ab54), 2025-03-26

[JarrettSJohnson]

This one still seems to be a bug. Thanks for the report.

Edit: Looks like this was just never supported because on headless we do CPU-ray tracing, and we don't yet support ray traced volumes.

[kmdalton]

Maybe irrelevant, but I am not explicitly calling "ray". Just using "draw" or directly calling "save filename.png". Maybe this triggers some sort of ray tracing internally. I can confirm that calling "ray" in the gui makes the volume disappear, but I am still able to save a (presumably non-raytraced) image by calling save. Thanks again for the speedy response on both issues 👍

[JarrettSJohnson]

No problem. I'll try summarize in case it's helpful to you or anyone else:

ray command will perform CPU-based ray tracing.

draw command will perform an OpenGL render with antialiasing via supersampling (draw at higher resolution and downscale to original).

save command with png extension from what I can tell will just copy whatever is on your screen and save it to desk as PNG format. So doing normal stuff in the workspace and immediately saving as .png, will just give you a drawn, rasterized image. If you do ray immediately followed by png, you'll see the ray-traced version saved as png.

png command will render out an image to disk. It has a ray flag that will determine whether to ray-trace or not. Rasterization is on by default.

When set ray_volume is set to 1 or on, whenever you ray trace an image with a volume in the workspace, an image of the volume (which is rasterized) will be blended onto that ray-traced image. But because this requires rasterization for volume, this is not available headless.

In the GUI, unless specified, rendering will be done by default with rasterization. Headlessly, because shaders are not available, all rendering is done via CPU ray-tracing.

A lot of this will likely change though for PyMOL 3.3