Details
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Type:
Bug
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Status: Closed
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Priority:
Blocker
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Resolution: Fixed
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Affects Version/s: 2.11.3.0, 2.11.3.1, 2.11.3.2
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Fix Version/s: 2.11.3.3
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Component/s: Command Line Interface, Structures
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Labels:
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Sprint:2.11.3.3 release
Description
Follow on from JAL-629 - giving a separate issue so we can report as known issue and resolve as a patch release if need be. Marked as blocker since this is a required capability for nf-core/proteinfold integration.
The following command line creates an image with plddt, secondary structure, and PAE annotation:
java -jar build/libs/jalview-all-TEST-j11.jar --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]examples/AlphaFold/AF-P00221-F1-model_v4.pdb --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=test-al-pae-ss.png --overwrite --gui
However, if --gui is removed, none of the 3d structure derived data are included in the exported figure.
The following command line creates an image with plddt, secondary structure, and PAE annotation:
java -jar build/libs/jalview-all-TEST-j11.jar --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]examples/AlphaFold/AF-P00221-F1-model_v4.pdb --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=test-al-pae-ss.png --overwrite --gui
However, if --gui is removed, none of the 3d structure derived data are included in the exported figure.
