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Opened 4 years ago
Last modified 4 years ago
#6581 feedback defect
Showing RMSD
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
When I run these commands:
mm #7,9,13,15,19 to #3/a show true
color byattribute seq_rmsd #3 palette blue:red:yellow
Will these show the average seq_rmsd of 7,9,13,15,19? Or will I just see the seq_rmsd of 19? If the average isn't shown, can this be implemented? This would be a nice feature for interpreting variability within a conformation. Also, the ability to obtain a seq_rmsd without alignment would be helpful.
Thanks,
Matt
Log:
> ui mousemode right "contour level"
> mousemode shift rightMode zoom
> set bgColor white
> graphics silhouettes true
> graphics silhouettes width 3
> hide all atoms
> style stick
Changed 0 atom styles
> style ions sphere
Changed 0 atom styles
> style ions sphere
Changed 0 atom styles
> show all cartoons
> show ligand target ab
> show ions atoms
> show sidechain & (ligand | ions) :< 3.5 target ab
> color /a #55c087
> color /b #ffe255
> color /c #f6986c
> color /d #6b80bc
> color /e #aa7fba
> color /g #FFC0CB
> color /h #b2b2b2
> color /i red
> color byhetero
> lighting soft
> lighting depthCue false
> cartoon suppressBackboneDisplay false
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
> alias sa isolde sim stop
> alias sb isolde sim stop discardTo start
> alias m2 matchmaker #2 to #1 & sel
> alias m3 matchmaker #3 to #1 & sel
> alias m4 matchmaker #4 to #1 & sel
> alias ct ui mousemode right "contour level"
> alias zm ui mousemode right zoom
> alias cr view $*; clip off; zoom .8
> alias iw isolde write phenixRsrInput #1 2.8 #1 includeH false
> alias rmp4 movie record; rock y 30 384 cycle 384; wait 384; movie encode
> "/Users/jaremko/cryoem/rock_movie.mp4"
> alias sc show (sel-residues & sidechain) target ab
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.7.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0)
OS Loader Version: 540.60.2~89
Software:
System Software Overview:
System Version: macOS 12.1 (21C52)
Kernel Version: Darwin 21.2.0
Time since boot: 6 days 23:03
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
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ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
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qtconsole: 5.1.1
QtPy: 1.11.3
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requests: 2.26.0
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sphinxcontrib-devhelp: 1.0.2
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sphinxcontrib-jsmath: 1.0.1
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tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (8)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Analysis |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Showing RMSD |
comment:2 by , 4 years ago
| Status: | accepted → feedback |
|---|
comment:3 by , 4 years ago
If you are using the daily build, you could use the "sequence align" command to generate an overall alignment.
--Eric
follow-up: 4 comment:4 by , 4 years ago
In case it wasn't clear, the RMSD actually comes from the sequence alignment window: in the general case (which could include different proteins with different sequences) an alignment is required to indicate which residue goes with which, i.e. which are in the same columns as each other. So you need a single alignment associated with all of the structures to give an overall alignment and overall RMSD. As Eric mentioned, you could either have an alignment window in which each structure is a separate sequence, or if the structures have very similar or the same sequence, you could simply show one sequence and associate all of the structures with that one sequence. Then show the RMSD header in that window and/or color by the resulting attribute values.
follow-up: 5 comment:5 by , 4 years ago
Hi Elaine,
Thanks! That's basically what I want to do. I have mutants with the same general conformation, but I want to see the variability by coloring through the overall seq_rmsd attribute. Can this all be done by the command line? Or do I have to work within the alignment window?
Thanks,
Matt
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, April 11, 2022 3:39:09 PM
To: pett@cgl.ucsf.edu; Jaremko, Matt
Cc: meng@cgl.ucsf.edu
Subject: Re: [ChimeraX] #6581: Showing RMSD
#6581: Showing RMSD
-----------------------------------------+----------------------
Reporter: jaremko@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Structure Analysis | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+----------------------
Comment (by Elaine Meng):
{{{
In case it wasn't clear, the RMSD actually comes from the sequence
alignment window: in the general case (which could include different
proteins with different sequences) an alignment is required to indicate
which residue goes with which, i.e. which are in the same columns as each
other. So you need a single alignment associated with all of the
structures to give an overall alignment and overall RMSD. As Eric
mentioned, you could either have an alignment window in which each
structure is a separate sequence, or if the structures have very similar
or the same sequence, you could simply show one sequence and associate all
of the structures with that one sequence. Then show the RMSD header in
that window and/or color by the resulting attribute values.
}}}
--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac_ChimeraX_ticket_6581-23comment-3A4&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=DgtnXLtX0PCn9-dhlZik685MvbG8KVRUtuPBiuGgBds&s=IjOieDVLagSlUzViJUZx4QzAQnQK_9Q-IdbJg9IIstQ&e= >
ChimeraX <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=DgtnXLtX0PCn9-dhlZik685MvbG8KVRUtuPBiuGgBds&s=7LBNkIRhtKiDKfRxZmi3T_t0pF6OPupFB1nTOafseM0&e= >
ChimeraX Issue Tracker
follow-up: 6 comment:6 by , 4 years ago
It might be easier through the GUI, as in less of of learning curve for the commands (and I believe you would still need to show the GUI) but yes, it can be done with commands. Here is a pairwise example where I match one conformation of a protein onto another and then show sequence for one and associate the other with the sequence, then show RMSD header, then use the resulting attribute. You would need to generalize; you already have the multiple superposition and only need to show the sequence of any one of those structures, but then would need to associate all of the others with that sequence (there would be multiple "seq associate" commands in your case). Here are the example commands: open 2gbp open 2fw0 mm #2 to #1 seq chain #1/A seq associate #2/A seq header rmsd show color byattribute seq_rmsd #2 palette 0,blue:3,red:10,yellow If you look at the sequence command help, these commands all allows specifying an alignment ID. I can omit it in this case because there is only one sequence window shown. You can also omit it similarly, if you only show one sequence window. Use command "help sequence" to see the help page for all these seq commands.
follow-up: 7 comment:7 by , 4 years ago
Hi Elaine, Great, thanks! I will try this. This should work with 3 or more structures also, right? I would use seq associate #2,3/a, for example? Thank you! Matt ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, April 12, 2022 11:29:17 AM To: ChimeraX-bugs@cgl.ucsf.edu Cc: pett@cgl.ucsf.edu; Jaremko, Matt Subject: Re: [ChimeraX] #6581: Showing RMSD It might be easier through the GUI, as in less of of learning curve for the commands (and I believe you would still need to show the GUI) but yes, it can be done with commands. Here is a pairwise example where I match one conformation of a protein onto another and then show sequence for one and associate the other with the sequence, then show RMSD header, then use the resulting attribute. You would need to generalize; you already have the multiple superposition and only need to show the sequence of any one of those structures, but then would need to associate all of the others with that sequence (there would be multiple "seq associate" commands in your case). Here are the example commands: open 2gbp open 2fw0 mm #2 to #1 seq chain #1/A seq associate #2/A seq header rmsd show color byattribute seq_rmsd #2 palette 0,blue:3,red:10,yellow If you look at the sequence command help, these commands all allows specifying an alignment ID. I can omit it in this case because there is only one sequence window shown. You can also omit it similarly, if you only show one sequence window. Use command "help sequence" to see the help page for all these seq commands.
follow-up: 8 comment:8 by , 4 years ago
My previous reply said you would have multiple "seq associate" commands, but yes, it is also possible just to give one "seq associate" command with multiple chains specified, as you suggest. If you want to associate the sequence with *all* of the "A" chain structures that are present in ChimeraX, you could even specify them collectively by omitting the model numbers, e.g. "seq associate /A" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#associate>
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Hi Matt,
--Eric