Opened 2 years ago

Closed 2 years ago

#10126 closed defect (fixed)

Phenix location

Reported by: swlovell@… Owned by: pett
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc: fatma@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.1.0-1025-oem-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202311080035 (2023-11-08 00:35:54 UTC)
Description
When trying to run em fitting with phenix, it asks for my phenix location.  I then enter the phenix path and run the fitting routine and the message shows up.  Could not find Phenix installation in /home/swlovell.
Use "phenix location" command to specify the location of your Phenix installlation. 

Log:
UCSF ChimeraX version: 1.7.dev202311080035 (2023-11-08)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open https://www.rbvi.ucsf.edu/chimerax/data/stanford-
> apr2022/cryoem_intro.html

Opened https://www.rbvi.ucsf.edu/chimerax/data/stanford-
apr2022/cryoem_intro.html  

> open 25428 fromDatabase emdb

Summary of feedback from opening 25428 fetched from emdb  
---  
notes | Fetching compressed map 25428 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-25428/map/emd_25428.map.gz  
Fetching map header 25428 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-25428/header/emd-25428.xml  
open kw {'initial_surface_level': 0.028}  
  
Opened emdb 25428 as #1, grid size 300,300,300, pixel 1.08, shown at level
0.028, step 2, values float32, fit PDB 7sth  

> volume #1 level 0.02089

> volume #1 level 0.01733

> volume #1 step 4

> volume #1 level 0.01409

> volume #1 step 16

> volume #1 step 2

> volume #1 step 1

> volume #1 level 0.01478

> volume #1 level 0.01202

> save test.png

> open 7sth fromDatabase pdb format mmcif

Summary of feedback from opening 7sth fetched from pdb  
---  
note | Fetching compressed mmCIF 7sth from
http://files.rcsb.org/download/7sth.cif  
  
7sth title:  
Full-length insulin receptor bound with unsaturated insulin WT (2 insulin
bound) symmetric conformation [more info...]  
  
Chain information for 7sth #2  
---  
Chain | Description | UniProt  
A B | Insulin receptor | INSR_MOUSE -26-1344  
C D | Insulin | INS_HUMAN -23-76  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #1 level 0.02236

> hide #!1 models

> hide cartoons

> show cartoons

> color bychain

> select /A:1-909

6629 atoms, 6810 bonds, 6 pseudobonds, 820 residues, 2 models selected  

> select /A:1-909

6629 atoms, 6810 bonds, 6 pseudobonds, 820 residues, 2 models selected  

> select /B:1-909

6629 atoms, 6810 bonds, 6 pseudobonds, 820 residues, 2 models selected  

> select /A:1-909

6629 atoms, 6810 bonds, 6 pseudobonds, 820 residues, 2 models selected  

> select /C:2-76

376 atoms, 386 bonds, 1 pseudobond, 48 residues, 2 models selected  

> select /D:2-76

376 atoms, 386 bonds, 1 pseudobond, 48 residues, 2 models selected  

> select clear

> show #!1 models

> hide #!1 models

> mlp

Map values for surface "7sth_A SES surface": minimum -29.01, mean -4.303,
maximum 23.94  
Map values for surface "7sth_B SES surface": minimum -29.37, mean -4.316,
maximum 26.11  
Map values for surface "7sth_C SES surface": minimum -29.57, mean -2.35,
maximum 21.92  
Map values for surface "7sth_D SES surface": minimum -27.87, mean -2.282,
maximum 22.49  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> show surfaces

> hide surfaces

> show #!1 models

> hide #!1 models

> show surfaces

> hide surfaces

> select clear

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select /D:19

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select down

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select down

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select down

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select up

90 atoms, 91 bonds, 12 residues, 2 models selected  

> select up

376 atoms, 386 bonds, 48 residues, 2 models selected  

> select up

14010 atoms, 14392 bonds, 1736 residues, 2 models selected  

> select down

376 atoms, 386 bonds, 48 residues, 5 models selected  

> select down

90 atoms, 91 bonds, 12 residues, 2 models selected  

> select down

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select up

90 atoms, 91 bonds, 12 residues, 2 models selected  

> hide ~sel ribbons

> show #!1 models

> ui tool show "Surface Zone"

> surface zone #1 nearAtoms sel distance 6.48

> surface zone #1 nearAtoms sel distance 3.2

> surface zone #1 nearAtoms sel distance 2.89

> volume #1 style mesh

> volume #1 style image region 0,0,149,299,299,149 step 1 showOutlineBox true

> volume #1 region 0,0,0,299,299,299 step 1

> volume #1 style mesh region 0,0,0,299,299,299 step 1

> show sel atoms

> color sel byhetero

> ui tool show AlphaFold

Fetching compressed P15208 UniProt info from
https://www.uniprot.org/uniprot/P15208.xml  

> alphafold match INSR_MOUSE

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold P15208 from
https://alphafold.ebi.ac.uk/files/AF-P15208-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: P15208 (UniProt INSR_MOUSE)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
INSR_MOUSE | INSR_MOUSE | 100.0 | 100.0  
Opened 1 AlphaFold model  

> hide #3 models

> hide #!2 models

> hide #!1 models

> show #3 models

> show #!2 models

> show #!1 models

Fetching PAE using AlphaFold database version 4  

> alphafold pae #3 uniprotId P15208 version 4

Fetching compressed AlphaFold PAE P15208 from
https://alphafold.ebi.ac.uk/files/AF-P15208-F1-predicted_aligned_error_v4.json  

> color #3:373-373 lime

> color #3:467-467 magenta

> color #3:364-373 lime

> color #3:470-473 magenta

> color #3:428-428 lime

> color #3:612-612 magenta

> color #3:425-425 lime

> color #3:387-389 magenta

> color #3:295-295 lime

> color #3:167-167 magenta

> color #3:337-531 lime

> color #3:506-506 lime

> color #3:520-520 magenta

> color #3:128-409 lime

> color #3:398-398 lime

> color #3:373-373 magenta

> color #3:931-1359 lime

> color #3:614-617 lime

> color #3:595-595 magenta

> color #3:642-820 lime

> color #3:39-373 magenta

> color #3:231-603 lime

> color #3:317-517 lime

> color #3:212-731 lime

> volume #1 region 0,0,0,299,299,299

> color #3:548-548 lime

> color #3:320-320 magenta

> delete #3:1-27,337-end

> surface zone #1 nearAtoms sel distance 2.9

> surface zone #1 nearAtoms sel distance 2.91

> surface zone #1 nearAtoms sel distance 2.92

> surface unzone #1

Drag select of 309 residues  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,66.855,0,1,0,162.5,0,0,1,124.11

> view matrix models #3,1,0,0,83.991,0,1,0,197.69,0,0,1,123.23

> view matrix models #3,1,0,0,105.6,0,1,0,194.51,0,0,1,102.93

> view matrix models #3,1,0,0,104.27,0,1,0,204.27,0,0,1,97.93

> fitmap #3 inMap #1

Fit molecule AlphaFold INSR_MOUSE (#3) to map emdb 25428 (#1) using 2462 atoms  
average map value = 0.02569, steps = 160  
shifted from previous position = 3.54  
rotated from previous position = 25.9 degrees  
atoms outside contour = 1380, contour level = 0.022363  
  
Position of AlphaFold INSR_MOUSE (#3) relative to emdb 25428 (#1) coordinates:  
Matrix rotation and translation  
0.89977287 0.30593894 -0.31114329 109.05998908  
-0.31542392 0.94872498 0.02070437 210.13887975  
0.30152369 0.07951280 0.95013745 95.38416111  
Axis 0.06724099 -0.70051753 -0.71046031  
Axis point 256.76280233 -317.99569276 0.00000000  
Rotation angle (degrees) 25.93148019  
Shift along axis -207.63932660  
  

> fitmap #3 inMap #1

Fit molecule AlphaFold INSR_MOUSE (#3) to map emdb 25428 (#1) using 2462 atoms  
average map value = 0.02569, steps = 48  
shifted from previous position = 0.0275  
rotated from previous position = 0.0667 degrees  
atoms outside contour = 1383, contour level = 0.022363  
  
Position of AlphaFold INSR_MOUSE (#3) relative to emdb 25428 (#1) coordinates:  
Matrix rotation and translation  
0.89961824 0.30545964 -0.31205998 109.02867755  
-0.31519581 0.94881405 0.02008747 210.13300179  
0.30222280 0.08028895 0.94985002 95.36412638  
Axis 0.06877674 -0.70178280 -0.70906323  
Axis point 256.35304276 -319.42927981 0.00000000  
Rotation angle (degrees) 25.95459558  
Shift along axis -207.58828507  
  

> view matrix models
> #3,0.89962,0.30546,-0.31206,106.6,-0.3152,0.94881,0.020087,211.74,0.30222,0.080289,0.94985,92.704

> view matrix models
> #3,0.89962,0.30546,-0.31206,106.79,-0.3152,0.94881,0.020087,209.6,0.30222,0.080289,0.94985,99.103

> view matrix models
> #3,0.89962,0.30546,-0.31206,107.01,-0.3152,0.94881,0.020087,209.52,0.30222,0.080289,0.94985,99.237

> view matrix models
> #3,0.89962,0.30546,-0.31206,107.06,-0.3152,0.94881,0.020087,209.87,0.30222,0.080289,0.94985,99.35

> view matrix models
> #3,0.85565,0.32697,-0.40119,107.75,-0.33788,0.94009,0.045535,210.24,0.39205,0.096596,0.91486,97.875

> view matrix models
> #3,-0.51898,0.41335,0.7482,138.41,-0.60984,0.4343,-0.66293,203.8,-0.59896,-0.80033,0.026685,97.029

> view matrix models
> #3,-0.51898,0.41335,0.7482,141.81,-0.60984,0.4343,-0.66293,204.06,-0.59896,-0.80033,0.026685,94.609

> ui tool show "Local EM Fitting"

Must specify a structure to fit  
Must specify exactly two half maps for fitting  
[Repeated 2 time(s)]

> ui tool show "Local EM Fitting"

> hide #!2 models

> show #!2 models

> hide #3 models

> show #3 models

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> ui mousemode right "move markers"

> marker change #4:1 position 125.5,190,91.84

> marker change #4:1 position 126.6,190,91.29

> marker change #4:1 position 128.1,189.4,92.5

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 128.142,189.363,92.4996 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  

> phenix location /home/swlovell/crystal/phenix

No Phenix installation found  

> ui tool show "Local EM Fitting"

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> marker change #4:1 position 108.8,156.3,115.8

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 108.81,156.277,115.827 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  

> location/home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix

Unknown command: phenix
location/home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix  

> ui tool show "Local EM Fitting"

[Repeated 1 time(s)]

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> marker change #4:1 position 110.1,157,117.5

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 110.08,156.992,117.506 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  

> phenix location
> /home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix

Using Phenix installation
/home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix  

> ui tool show "Local EM Fitting"

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> marker change #4:1 position 111.1,154.5,115.8

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 111.148,154.453,115.842 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  

> phenix location
> /home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix

Using Phenix installation
/home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix  

> ui tool show "Local EM Fitting"

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> marker change #4:1 position 111.7,155.7,117.5

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 111.674,155.717,117.485 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  

> "phenix location"
> /home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix

Unknown command: "phenix location"
/home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix  

> phenix location
> /home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix

Using Phenix installation
/home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix  

> ui tool show "Local EM Fitting"

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> marker change #4:1 position 114.4,156,119.9

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 114.445,155.988,119.885 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  

> phenix location /crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> ui tool show "Local EM Fitting"

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> marker change #4:1 position 111.1,157.5,118.8

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 111.089,157.469,118.75 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  

> phenix location
> /home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix

Using Phenix installation
/home/swlovell/crystal/phenix/phenix-1.21rc1-5127/build/bin/phenix  

> ui tool show "Local EM Fitting"

> marker #4 position 161.46,161.46,161.46 radius 41.7993 color 100,65,0,50

> marker change #4:1 position 109.4,157.9,117.9

> phenix emplaceLocal #3 mapData #1 resolution 3.5 center
> 109.43,157.926,117.92 showSharpenedMap false

Could not find Phenix installation in /home/swlovell.  
Use "phenix location" command to specify the location of your Phenix
installlation.  




OpenGL version: 4.6 (Core Profile) Mesa 23.0.4-0ubuntu1~22.04.1
OpenGL renderer: Mesa Intel(R) Graphics (RPL-S)
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=lxqt
XDG_SESSION_DESKTOP=lxqt
XDG_CURRENT_DESKTOP=LXQt
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 7680
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 28 13th Gen Intel(R) Core(TM) i7-13850HX
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       2.1Gi        24Gi       499Mi       4.4Gi        28Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:a788] (rev 04)	
	Subsystem: Dell Device [1028:0c41]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.13.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.7.22
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.12
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.50
    ChimeraX-AtomicLibrary: 12.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202311080035
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.1
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.12
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.13
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.44.0
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.11.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.0.7
    wcwidth: 0.2.9
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (5)

comment:1 by pett, 2 years ago

Component: Unassigned → Structure Analysis
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Phenix location

comment:2 by pett, 2 years ago

Resolution: → not a bug
Status: accepted → closed

Hi Scott,

Thanks for reporting this problem. I will try to improve the "phenix location" to clarify what argument it needs, but what it needs is the top-level directory that Phenix created when it was installed. So in your case I believe the correct command would be:

phenix loc /home/swlovell/crystal/phenix/phenix-1.21rc1-5127

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Zach Pearson, 2 years ago

Resolution: not a bug
Status: closed → reopened

I think this is a real bug. I was trying to help someone run this on Windows and their machine didn't respond to changes in the Phenix installation location -- fitting always errored out and reported C:\Users\<username>

Shouldn't all the calls to find_phenix_command use the setting?

comment:4 by Zach Pearson, 2 years ago

Cc: fatma@… added

comment:5 by pett, 2 years ago

Resolution: → fixed
Status: reopened → closed

Some code to better handle Windows installations didn't make it into the 1.2.0 release. Just made a 1.2.1 release which includes the improved code which should rectify this problem.

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