id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3344 Opening structure-factor cif Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0rc202005270557 (2020-05-27 05:57:28 UTC) Description I might be mistaken, but I vaguely recall Eric saying that the new Open/Save framework should be able to distinguish between different file types with the same extensions based on arguments, but that doesn't seem to be the case here. If I register Clipper as a Provider to open cif format: ... then it appears to entirely override the atomic mmCIF format. Will disable it (it's still available as the ""clipper open"" command as always). Log: UCSF ChimeraX version: 1.0rc202005270557 (2020-05-27) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3io0.pdb 3io0.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for 3io0.pdb #1 --- Chain | Description A | predicted microcompartment protein > open 3io0-sf.cif structureModel #1 Summary of feedback from opening 3io0-sf.cif --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma, pdbx_anom_difference, pdbx_anom_difference_sigma, intensity_meas, intensity_sigma, pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma Automatically choosing ""intensity_meas, intensity_sigma"". notes | Resolution: 3.003 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... 3io0.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for 3io0.pdb --- Chain | Description 1.2/A | predicted microcompartment protein Opened crystallographic dataset from 3io0-sf.cif Found experimental reflection data: intensity_meas, intensity_sigma French and Wilson Amplitudes Rwork: 0.2014; Rfree: 0.2106 Generated maps: Reflection Data (LIVE) 2mFo-DFc (LIVE) mFo-DFc (LIVE) 2mFo-DFc_sharp_29 Any unwanted maps may be safely closed via the Model panel. > open 3io0-sf.cif Must specify a structure model to associate with crystallographic data > open 3io0.cif Must specify a structure model to associate with crystallographic data > save test.mtz Writing data to: '/*/*/[FOBS, SIGFOBS]' > save test.mtz #1 Writing data to: '/*/*/[FOBS, SIGFOBS]' OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 5.2G 46G 298M 10G 56G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Input/Output not a bug Tom Goddard all ChimeraX