- ChimeraX-users - RBVI Mailing Lists

Question about Space navigator and ChimeraX
by Tweten, Rodney K. (HSC) 25 May '18

25 May '18

I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! [cid:image001.png@01D3F428.99CAA4A0] Cheers, Rod Tweten, Ph.D. George Lynn Cross Professor "It's a great life if you don't weaken" Microbiology & Immunology BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1 Email: rod-tweten(a)ouhsc.edu

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info selection
by Wei Wang 14 May '18

14 May '18

Hello, After using ctrl-left click to select an atom, I use “info selection” as instructed in the manual. However I received the following error message: TypeError: 'str' object is not callable File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/list_info/util.py", line 50, in spec return o.atomspec() See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. If I use “info selection atom” then: info selection <help:user/commands/info.html#selection> atom Expected a keyword What am I doing wrong with? Please advice. Best, Wei

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setattr m stickScale
by Wei Wang 14 May '18

14 May '18

Hello, I’m switching from Chimera1. I used to have “setattr m stickScale 0.6” to make whole stick representation “thinner”. Now in ChimeraX “stickScale” seems not available. Using “size stickRadius” looks similar to “setattr b radius” in Chimera1, but in this case the solvents radius are not changed. Is there a method to set all stick representation in the same arbitrary scale? Many thanks Wei

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How to import chimera session to chimeraX
by Liz Kellogg 03 May '18

03 May '18

Hi all I love the graphics in chimera X, and I would like to render a scene I've set up in chimera. However, chimeraX doesn't seem to be able to open chimera session files. I tried exporting the chimera scene to different file format, such as vtk or wrl, but chimeraX can't seem to open those files either. Is there any way to open chimera sessions in chimeraX? Thanks a lot Liz

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Re: [chimerax-users] spin movie error
by Sven Lange (PG Research) 02 May '18

02 May '18

Hi, I ran into the same error (related to _clock_gettime) today on macos 10.11, but found a workaround. I build ffmpeg using homebrew (brew -v install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265) and then replaced the ChimeraX.app/Contents/bin/ffmpeg with the homebrew ffmpeg. Movies encoding now works in ChimeraX on my macos 10.11. Best wishes Sven The University of Dundee is a registered Scottish Charity, No: SC015096

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mutitouch mac
by Edoardo Gianni 01 May '18

01 May '18

Hello, I was wondering if multitouch was available on chimerax for mac, or if you had plans to implement it in the future. Thanks and best wishes, Edoardo

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Change the size of the model
by Shuto Araki 01 May '18

01 May '18

Dear Chimera X developers, I am trying to create a VR protein tour video by using the movie command. There is no problem and it works perfectly fine, but I was wondering if I could change the size of molecule models themselves so that, when the camera is inside a model, I can look around the inner structure of the model with the surface further placed. Right now, the model is so small that the surface feels too close to the camera when it is inside the model. Is it possible to change the size of a model with the coordinate being fixed? Thanks, Shuto

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Equivalent of surface colour by radius in tools/Volume viewer of Chimera
by Shabih Shakeel 17 Apr '18

17 Apr '18

Hi, In ChimeraX, is there an equivalent of surface colour by radius in tools/Volume viewer of Chimera? I would like to colour an EM density map of a virus from its centre to the outside of the capsid with direct colour range in ChimeraX. Thanks. Regards, Shabih

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Re: [chimerax-users] [Chimera-users] ConSurf script on ChimeraX
by Eric Pettersen 10 Apr '18

10 Apr '18

Hi Fabian, As a stopgap, you can color by bfactor by using a script I’ve attached. I’m attaching two scripts, one a generic color-by-bfactor that can be used for anything in the bfactor column. You would edit the values at the top of the script to choose low-high coloring or low-mid-high coloring, and what values to associate to what colors. The other script is tailored to ConSurf output in that it knows the nine ConSurf colors and colors only those residues whose bfactors are all equal and are integers in the range 1-9. You just open the ConSurf-generated PDB and then open the script (which runs it). I’ve attached an example output image (2gbp). —Eric > On Apr 10, 2018, at 12:26 AM, Fabian Glaser <fabian.glaser(a)gmail.com> wrote: > > Dear Eric, > > Thanks for your detail answer, so maybe the only thing it will be really useful now is to be able to color the residues with consurf colors in ChimeraX, with that I will be able to make figures for a paper, which is what I am after at this point. > > Of course we would be very happy to get a script for ChimeraX at some point that could be included in our output pages. > > Best, > > Fabian > > Fabian Glaser PhD > > Head of the Structural Bioinformatics section > Bioinformatics Knowledge Unit - BKU > The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering > Technion - Israel Institute of Technology, Haifa, Israel > Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> > Tel +972 (0) 4 8293701 > > >> On 10 Apr 2018, at 1:59, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> >> Hi Fabian, >> ChimeraX is not backwards compatible with Chimera, so a Chimera session file cannot be opened in ChimeraX — such as what you tried to do below. We want to add a tool to Chimera that will write out a file that ChimeraX can read to restore the Chimera session as best it can, but we haven’t gotten there yet. >> Furthermore, although ChimeraX can display sequence alignments, its capabilities in that regard are currently much less than what Chimera offers. The features it lacks that ConSurf uses are: >> >> 1) Read Clustal ALN alignments >> 2) Show alignment headers >> 2b) Make header values available as residue attributes >> 3) Show Phylogeny trees >> 4) Color alignment/structures from coloring file >> >> To show ConSurf results in even bare bones form would require #1 and #4, and obviously #2 and #3 add a lot of value. So I’d say ChimeraX is not “ConSurf ready” yet. What I will do is open an “enhancement request” ticket in our bug database with you on the recipient list. As the above features get added I will update the ticket and at whatever point you feel it’s worthwhile you could work on getting ConSurf to deliver ChimeraX results. I would help with any questions or issues that popped up. Sorry I don’t have better news. >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >>> On Apr 8, 2018, at 7:56 AM, Fabian Glaser <fabian.glaser(a)gmail.com <mailto:fabian.glaser@gmail.com>> wrote: >>> >>> Hi, >>> >>> I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX >>> >>> ModuleNotFoundError: No module named 'cPickle' >>> >>> File "consurf_final_zn.py", line 1, in >>> >>> See log for complete Python traceback. >>> >>> If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. >>> >>> Is this something that can be fixed or updated? >>> >>> More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that? >>> >>> Here is the beginning of the original chimera script >>> >>> import cPickle, base64 >>> try: >>> from SimpleSession.versions.v65 import beginRestore,\ >>> registerAfterModelsCB, reportRestoreError, checkVersion >>> except ImportError: >>> from chimera import UserError >>> raise UserError('Cannot open session that was saved in a' >>> ' newer version of Chimera; update your version') >>> checkVersion([1, 12, 41623]) >>> import chimera >>> from chimera import replyobj >>> replyobj.status('Restoring session...', \ >>> blankAfter=0) >>> replyobj.status('Beginning session restore...', \ >>> blankAfter=0, secondary=True) >>> beginRestore() >>> >>> def restoreCoreModels(): >>> from SimpleSession.versions.v65 import init, restoreViewer, \ >>> restoreMolecules, restoreColors, restoreSurfaces, \ >>> restoreVRML, restorePseudoBondGroups, restoreModelAssociations >>> molInfo = >>> >>> Thanks a lot, >>> >>> Best, >>> >>> Fabian >>> >>> Fabian Glaser PhD >>> >>> Head of the Structural Bioinformatics section >>> Bioinformatics Knowledge Unit - BKU >>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering >>> Technion - Israel Institute of Technology, Haifa, Israel >>> Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> >>> Tel +972 (0) 4 8293701 >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >> >

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Re: [chimerax-users] [Chimera-users] CjimeraX PDB save
by Eric Pettersen 02 Apr '18

02 Apr '18

Hi John, The PDB format only supports single-character chain IDs (one of the reasons for mmCIF format), so it is impossible to save structures with more than 36 chains in PDB format without losing chain information. A semi-workaround is to: 1) In ChimeraX: split the structure into multiple structures, one per chain (“split #1”) 2) Save those models into a multi-MODEL PDB file (“save ~/rib.pdb models #1”) 3) Read them into Chimera. 4) If there are <= 36 models, combine them into a single model (“combine” button of the Model Panel), otherwise you just have to work with them as separate models. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Apr 2, 2018, at 2:29 PM, John Mercer, Ph.D. <jmercer(a)duke.edu> wrote: > > Hi Elaine, > > I load a ribosome mmcif file in ChimeraX and save it at as a PDB file. It loads and works fine in Chimera but all the chain identifiers have disappeared. Is there away to save a PDB file from ChimeraX that retains the identifiers? I am wanting to use the larger set of tools in Chimera when only mmcif files are available. > > Best, > -John > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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morph and surfaces
by Giorgio Luciano 02 Apr '18

02 Apr '18

Hello ! I was looking at the script for morphing among structures that can be found here http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html (*coordset #1 1,161). * I've tried to use the surfacecat command in the script in order to obtain a morph through volumes since my idea was to create the movie and then export all the surface perframe in order to use them in another 3d software. I've seen that surfcat can actually create volumes for all the surfaces included in the 1r7w but morph start does not seems to work among the surface created. I've seen also that it could be a solution to create density maps from the surface and them morph them using volume viewer but it seem quite an awkard solution (at least for me that I'm no expert :) I've tried to find the limitation of morph command but it does not report anything regarding surfaces. Any help is very appreciated. Sorry for the cross-posting

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I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by JEAN-YVES SGRO 29 Mar '18

29 Mar '18

Greetings, thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page help:user/autostyle.html with these details about the number of chains. As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost. e.g. simply by clicking on the "Show atoms" button in the Molecular display toolbar and then the "Hide atoms". I found commands for selection at http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html which are useful and one can reconstruct the initial display. As I example I am using myoglobin (1mbo.) The molecule opens as a ribbon, heteroatoms as stick models, the iron ion as sphere, and AA close to the ligands as sticks as well. Simply pressing the "Show atoms" button will display all water molecules as small spheres. But now if I click "Hide atoms" only the ribbon is left. Yesterday I tried to find a way to select heteroatoms in general and use the sel ~ sel selection inversion found on the pipermail<http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html> but that was not the best solution. Today I could reconstruct the initial display with these commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons: show ions show ligand select ligand:<3.8 & protein show selAtoms For novices this is a bit complicated to understand. Therefore I would like to suggest the addition of a "Automatic Styling (Smart Initial Display)" button, perhaps at the First position in the Molecular display toolbar. I firmly believe that this would avoid lots of frustration for many new users! P.S. One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? Sincerely, Jean-Yves Sgro

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Export as .obj
by Boris Chaumette 28 Mar '18

28 Mar '18

Dear colleagues, I am currently using ChimeraX and would like to save my file as a .obj I tried the following command line: save "ATPtest.obj" obj But model is expected. I don't understand how I can specify it to incorporate the whole figure. Thank you, Best, Boris Chaumette MD/PhD - postdoctoral researcher Laboratory of Guy A. Rouleau Montreal Neurological Institute McGill University Irving Ludmer Building 1033, Pine av. Room: 327 Montréal, Québec, H3A 1A1 Phone: +1 514-398-6821

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Matrixset equivalent
by Reza Khayat 15 Mar '18

15 Mar '18

Hi, Is there a matrixset (from Chimera) equivalent for ChimeraX? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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VR mode not working
by Sebastian Poelsterl 13 Mar '18

13 Mar '18

Hi, I'm trying to view a PDB structure (2fha) in vr mode, but get the following error after executing 'vr on': An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. Traceback (most recent call last): File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 61, in draw_new_frame view.draw(check_for_changes = False) File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\view.py", line 178, in draw r.draw_background() File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\opengl.py", line 677, in draw_background GL.glClear(flags) File "zr\accelerate\src\errorchecker.pyx", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError (src\errorchecker.c:1270) OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glClear, cArguments = (16640,) ) I'm using ChimeraX 0.5 with an Oculus Rift (1.24.0.545657), NVIDIA GeForce GTX 1060 (driver version 391.01) and SteamVR Version 2018-02-10 (1518226924) under Windows 10 (10.0.0.14393). Any suggestions would be appreciated. Thank you. Sebastian The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Some core modules moving
by Eric Pettersen 07 Mar '18

07 Mar '18

Hi all, In the interest of making ChimeraX’s core smaller and less likely to need frequent updating (since it can’t be updated incrementally via the ToolShed), we will be moving some modules out of the core and into bundles, so those at least will be individually updatable via the ToolShed. Those core modules are atomic, map, surface, and ui. As of tomorrow’s daily build, you can and should use the the new import paths for these modules (e.g. from chimera.atomic import Atom rather than from chimerax.core.atomic import Atom). Old-style imports will continue to work for several months at least, at which time a warning will be raised if the import is still in use (but the import will work). Probably several months after that we will disable the old-style imports. One further note is that the MainToolWindow class can now be imported directly from the ui module, rather than from its gui submodule, so: from chimerax.ui import MainToolWindow is preferred over: from chimerax.ui.gui import MainToolWindow —Eric Eric Pettersen UCSF Computer Graphics Lab

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Surfaces & color by attribute
by Hernando J Sosa 06 Mar '18

06 Mar '18

Dear ChimeraX Is it possible to color a surface by atom/residue attribute (hydrohobicity, charge)? I know it is possible to do it in ucsf-chimera but unfortunately surface calculation does not work in chimera for the files I am working on. Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa(a)einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>

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Cororing by B-factor
by Rajiv G Govindaraj 23 Feb '18

23 Feb '18

Hello, I am NOT able find the coloring atoms by bfactor in ChimeraX. I have a b-factor values range from negative to positive, and wants to color them from min to max(blue to red) as normal bfactor colors. Appreciated if you could tell me how it can be done in ribbons and surface using ChimeraX? Thank you. Regards, RJ

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ChimeraX user guide display issue
by Jerry Honts 19 Feb '18

19 Feb '18

Unlinked and linked text is *invisible* in user guide (and elsewhere in interface) because font color is *white* on white background. The apparently invisible text can be selected and displayed after copy and paste to another text field. Hyperlink underlines remain visible. Is this a CSS style sheet problem? Jerry E. Honts -- Jerry E. Honts, Ph. D. Associate Professor of Biology Drake University 2507 University Avenue Olin Hall 324 (office)

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open local pdb files "containing no atoms and bonds"
by Fekete Attila 15 Feb '18

15 Feb '18

Dear Colleagues, I have tried to open several local *.pdb files, but in each case I got the error: "Opened PDB data containing 0 atoms, 0 bonds and 0 coordinate sets", and a series of warnings (for each lines of the files) and ChimeraX doesn't show the structure. I have also tried different versions of ChimeraX (0.1/0.5 and even alpha releases, recently I'm using 0.5 under Ubuntu 16.04). I can open any online files (*pdb,*mmCIF) from the RCSB database, however if I download the same file, I got the above mentioned error message, so I have absolutely no clue to resolve the problem because I suppose this isn't related to pdb format issues but a bug can be somewhere in the softwere. I am really impressed by the visualization capabilities of ChimeraX so please help me if you can. Yours, Attila

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ChimeraX surface coloring
by Nadishka Jayawardena 14 Feb '18

14 Feb '18

Hi there, I recently installed ChimeraX and been trying to figure out a way to colour a cryo-EM map by radius- however, I couldn't find a way to get this done? Is this feature not implemented on ChimeraX as yet? Is there a way to colour the map by using a python script? Many thanks Nadishka P.S. Must say that this new version is a huge improvement!

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spin movie error
by Andrey Feklistov 05 Feb '18

05 Feb '18

Dear chimera X developers, upon trying to record a spin movie with a corresponding button I get an error: dyld: Symbol not found: _clock_gettime,Referenced from: /Volumes/ChimeraXInstaller 2/ChimeraX.app/Contents/bin/ffmpeg,Expected in: /usr/lib/libSystem.B.dylib Typing the command manually results in the same error. I remember that the feature used to work when I first tested ChimeraX last year. Thanks for any advice.. Andrey

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2dimage?
by Emmott, Ed 31 Jan '18

31 Jan '18

Hi, Is there (or likely to be in future) a 2d image feature, allowing you to overlay 2d graphics (.tif, .png) in the same way as the 2dlabel command (e.g. Xpos Ypos )? My use case is wanting to add additional 2d graphics (e.g. color bar or graphs) over a pdb structure prior to rendering images/generating movies. Whilst I can get ChimeraX to open the images easily e.g. (open "...test.tif"), they are acquiring edges (white background image on white background scene -> grey borders) I assume as a result of being interpreted as a 3d object. Otherwise loving the software! Thanks a lot, Ed Using ChimeraX build v0.5 (2018-01-12) Dr Edward Emmott Research Associate Slavov Lab Northeastern University 332 Mugar, 360 Huntington Ave. Boston, MA.

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Ignored bad PDB record found
by Maurício Menegatti Rigo 31 Jan '18

31 Jan '18

I don't understand, my .pdb file seems perfectly fine, but I keep getting this error: *Ignored bad PDB record found on line 1ATOM 1 N ASN A 1 61.433 13.168 52.787 1.00 69.56 N Ignored bad PDB record found on line 2ATOM 2 CA ASN A 1 62.543 13.695 51.962 1.00 69.56 C Ignored bad PDB record found on line 3ATOM 3 C ASN A 1 61.990 14.337 50.735 1.00 69.56 C Ignored bad PDB record found on line 4ATOM 4 O ASN A 1 60.999 13.878 50.167 1.00 69.56 O Ignored bad PDB record found on line 5ATOM 5 CB ASN A 1 63.479 12.547 51.555 1.00 69.56 C2610 messages similar to the above omitted* I can open it in Chimera, PyMol, VMD, among others. But in ChimeraX is always the same error. I'm working on Linux (Ubuntu 14.04) with ChimeraX version 0.5 (2018-01-24). Any help? Thanks in advance, Mauricio M Rigo, Ph.D

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Consultation about software use
by dejesusm＠sloankettering.edu 30 Jan '18

30 Jan '18

Good day. I am Miguel de Jesus, a graduate student in the lab of Morgan Huse at the Sloan-Kettering Institute, NY. We are embarking on a new project that may require some sophisticated analysis of morphology from time-series imaging data. I have encountered a recent paper (Fritz-Laylin et al., eLife 2017) that used UCSF ChimeraX to analyze lattice light sheet data on neutrophils. I suspect my project may benefit from the same tools, but I have no experience with computational or image analysis as of yet. Would it be possible for me to consult with someone from the dev team, perhaps over Skype or e-mail, to ask rather rudimentary questions about how I might be able to conduct analysis for the planned work? Thanks so much. Miguel DJ Miguel Francisco M. de Jesus Graduate Student (Huse Lab) Memorial Sloan Kettering Cancer Center Zuckerman Research Center, 417 E 68th Street, New York City, NY 10065, USA

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