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  1. Jalview
  2. JAL-4344

--structureimage is only creating a background coloured square image when run through the installer shell script (jalview.sh)

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      Description

      When creating a structure image on the command line using the installer provided shell script, e.g.

      jalview --open ./examples/uniref50.fa --structure ./examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL --colour gecos-ocean --structureimage temp1.png --bgcolour red --overwrite

      the image produced only contains the background colour, and no structure.

      If you run the very same command that jalview.sh runs straight from the command line then the image is produced correctly. You can obtain the command that jalview.sh runs by adding --debug and looking for

      Shell running: "/Applications/..." ... --debug

      Note, copy everything from the opening quotation mark to the final --debug (without a quotation mark -- the quotes are closed around the java command and some of the arguments but not all).

      Running this command on the command line produces a correct structure image.

      jalview.sh does not set any environment variables.

      --image correctly produces alignment images.

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            Assignee:
            soares Ben Soares
            Reporter:
            soares Ben Soares
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