id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3423 Cannot save PIR andrea.graziadei@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-72-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Sequence alignment save pir format not working. If i click on a sequence and do file->save as NBRF/PIR the command does not work. the log shows the command as save /home/andrea/Dropbox/Cullin_Andrea/build_missing/test.pir format NBRF/PIR alignment full.fa-3 when i believe it should be save /home/andrea/Dropbox/Cullin_Andrea/build_missing/test.pir format pir alignment full.fa-3 Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open full.fa alignment false Summary of feedback from opening full.fa --- notes | Alignment identifier is full.fa-1 Alignment identifier is full.fa-2 Alignment identifier is full.fa-3 Alignment identifier is full.fa-4 Alignment identifier is full.fa-5 Opened 5 sequences from full.fa > open /home/andrea/Dropbox/Cullin_Andrea/build_missing/state-3_fit-chains.pdb Chain information for state-3_fit-chains.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available G | No description available Associated state-3_fit-chains.pdb chain G to CUL4 with 0 mismatches Associated state-3_fit-chains.pdb chain B to DCAF1 with 3 mismatches Associated state-3_fit-chains.pdb chain D to ROC1 with 0 mismatches Associated state-3_fit-chains.pdb chain C to Vpr with 0 mismatches > sequence associate /A full.fa-3:1 Associated state-3_fit-chains.pdb chain A to DDB1 with 8 mismatches and/or gaps > save /home/andrea/Dropbox/Cullin_Andrea/build_missing/test.pir format > NBRF/PIR alignment full.fa-3 Invalid ""format"" argument: Should be one of 'bmp image', 'brix', 'cmap', 'dcd', 'fasta', 'gif image', 'gltf', 'imagic', 'jpeg image', 'markers', 'mmcif', 'mol2', 'mrc', 'obj', 'pdb', 'pir', 'png image', 'ppm image', 'pseudobonds', 'rsf', 'segger', 'session', 'stl', 'tiff image', 'vtk', or 'x3d' > save /home/andrea/Dropbox/Cullin_Andrea/build_missing/test format NBRF/PIR > alignment full.fa-3 Invalid ""format"" argument: Should be one of 'bmp image', 'brix', 'cmap', 'dcd', 'fasta', 'gif image', 'gltf', 'imagic', 'jpeg image', 'markers', 'mmcif', 'mol2', 'mrc', 'obj', 'pdb', 'pir', 'png image', 'ppm image', 'pseudobonds', 'rsf', 'segger', 'session', 'stl', 'tiff image', 'vtk', or 'x3d' > save /home/andrea/Dropbox/Cullin_Andrea/build_missing/test.pir format pir > alignment full_fa Invalid ""alignment"" argument: No known alignment with ID: 'full_fa' > save /home/andrea/Dropbox/Cullin_Andrea/build_missing/test.pir format pir > alignment full.fa Invalid ""alignment"" argument: No known alignment with ID: 'full.fa' > save /home/andrea/Dropbox/Cullin_Andrea/build_missing/test.pir format pir > alignment full.fa-3 OpenGL version: 3.3.0 NVIDIA 440.64 OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: PC Specialist LTD Model: OptimusIX 15 OS: Linux Mint 19.1 tessa Architecture: 64bit ELF CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz Cache Size: 9216 KB Memory: total used free shared buff/cache available Mem: 31G 4.6G 20G 183M 5.7G 25G Swap: 31G 0B 31G Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b] Subsystem: CLEVO/KAPOK Computer Device [1558:852b] Kernel driver in use: i915 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Sequence 1.0 fixed all ChimeraX