- ChimeraX-users - RBVI Mailing Lists

cut-through session color
by Steve Chou 15 Jun '20

15 Jun '20

Dear ChimeraX developers and users, Is it possible to define the color surface cut-through sessions? Thanks in advance! Steve -- Steve Chou

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Cupy dependency for ChimeraX bundle
by Arthur Ecoffet 09 Jun '20

09 Jun '20

Hi, I am currently trying to develop a bundle for ChimeraX and the methods implemented can both run on GPU (using Cupy with a Cuda dependency) or on CPU. I am wondering how to deal with this "pseudo-dependency" with cupy, since it is not necessary to run the code but it is more computationally efficient. If a Cupy dependency is written in the "bundle_info.xml" file, will it create errors for computers without Nvidia Cuda installed ? Is there any way for users to install supplemental package by hand directly in chimeraX python as it was possible with Chimera ? Or is the only solution to add by hand a dependency line in the xml file ? Thanks, Arthur

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Volume series
by Kotaro TANAKA 09 Jun '20

09 Jun '20

Hi, I'm trying to create a morphing movie of a series of 3D maps. For that purpose, if I understand correctly, I need a volume series (vseries) of those maps, and according to the documentation (https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html#vseries) I should obtain a volume series simply by opening the maps at once in a file opening dialogue. I attached a screen shot of the Models panel after opening my maps, and my question is, are those maps already consisting a volume series? vseries commands fail with 'No volume series specified' I would appreciate your comments, thank you Best regards, Kotaro

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Deleting regions of whole protein
by Anas Hussain 08 Jun '20

08 Jun '20

Hello, I am currently working on a projectpertaining to the Corona Virus. I was wondering if there is anyway I could delete parts of awhole protein using the ChimeraX software. Thank you, Dr. Anas Hussain.

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mesh grid sampling
by Steve Chou 08 Jun '20

08 Jun '20

Dear ChimeraX developers and users, I'm trying to display a map as mesh in ChimeraX, but the grid sampling is too sparse. *volume #1 style mesh level 0.02 step 1 color blue* Is there a way to increase the grid sampling, so that the chicken wires look denser? Thanks in advance! Steve -- Steve Chou

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developing bundles autocompletion
by Daniel Esteban Palma Igor 06 Jun '20

06 Jun '20

Hi, normally I use spyder for writing python code, is there a way to have autocompletion of functions and modules when developing a bundle for ChimeraX? Any other tips for development is well received. Regards, Daniel Palma Igor

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2D and 3D objects
by Jazzar, Rodolphe 04 Jun '20

04 Jun '20

Hi, First of all, this is a great program, and I am barely using it to full extent of its possibilities. I am currently interested in combining a 3D object (a molecule.pdb) and a 2D object/plane/image (as a .png or any other). The idea being that I want to show a slice of an ELF plot, with the 3D molecule embedded through the 2D plot. Good news is that I can import both objects (.pdb and .png). However I face a size issue with the 2D object, which is considerably bigger than the 3D one. Would you know if I can size down a 2D object, or enlarge a 3D one respectively. All in all would you know if chimeraX can generate something like the picture attached by combining a 2D and a 3D object. Thanks for your time, Cheers, Rodolphe [cid:D31DAF51-91B8-4F78-94B3-4C0FCD9C860E] Dr. Rodolphe Jazzar, CNRS Research Associate - (French National Centre for Scientific Research) UCSD-UMI 3555 ORCID : 0000-0002-4156-7826 Office: (858)-534-5315 Mobile: 858-337-2228 University of California, San Diego, 5213 Pacific Hall, Department of Chemistry, 9500 Gilman Dr, # 0343, La Jolla, CA 92093-0343 http://bertrandgroup.ucsd.edu<http://bertrandgroup.ucsd.edu/> https://northamerica.cnrs.fr<https://northamerica.cnrs.fr/> http://www.cnrs.fr/en/cnrs [cid:image001.png@01CFDE12.00855770]

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Re: [chimerax-users] ChimeraX cross links
by Elaine Meng 04 Jun '20

04 Jun '20

> On Jun 4, 2020, at 1:25 AM, Dina Schneidman <duhovka(a)gmail.com> wrote: > > Hi, > We are getting addicted to the ChimeraX graphics, amazing! > I couldn't find how to add cross-links on top of the structure. What would be the best way to do this? > Also, is there a way to color different cross-link types in distinct colors? > Thanks and stay safe! > Dina Hi Dina, Glad you like it, and I certainly hope you and your family are staying safe too! As I understand it there are two ways for atomic structures with crosslinks to be shown in ChimeraX: (1) some integrative modeling structures include such crosslinks. If you download the "cif" from the PDB IHM site <https://pdb-dev.wwpdb.org/> and then change its filename suffix to "ihm" instead, then you can open it in ChimeraX. If the IHM model has crosslinks, they should show up somewhere in the model hierarchy of that data, which you can explore in the Models panel. An example of one with crosslinks is the BBSome: <https://pdb-dev.wwpdb.org/entry.html?PDBDEV_00000018> (2) or if you just have any atomic structure already in ChimeraX and you want to add crosslinks, you can read in pseudobond file (filename.pb), which is just a series of atom-pair specifications in plain text. You can also include color, radius, number of dashes. The file description is the bottom section of this page: <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> Also, you can change colors, number of dashes, and radius of any pseudobonds already in the structure or previously added, just using the commands "color" "style" and "size"; see the links in the top section of the pseudobonds page. There is a chimerax mailing list CC-d here for questions (unless they contain private data). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Installation of ChimeraX in Centos 7
by Gaya Yadav 01 Jun '20

01 Jun '20

?Dear Sir/Madam, I am trying to install Chimera X in the Centos 7 in my local directory. I installed it by converting it chimerax-rc.cpio?. But I cannot launch it, it was showing error about the openGL. Is that because of the openGL or it is not installed properly? Here is the error: WARNING: QXcbConnection: XCB error: 145 (Unknown), sequence: 178, resource id: 0, major code: 139 (Unknown), minor code: 20 NOTE: available bundle cache has not been initialized yet ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4 Try updating your graphics driver. WARNING: The X11 connection broke: No error (code 0) XIO: fatal IO error 0 (Success) on X server "localhost:12.0" after 668 requests (668 known processed) with 0 events remaining. ? Thanks Gaya

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Source Code
by Dario Eltzner 29 May '20

29 May '20

Hello, I was interested in reading the ChimeraX source code but found only this site https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html which references a git repo that is password protected. Is the source code not freely available? Best Wishes Dario Eltzner

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Re: [chimerax-users] 3D stereo lighting is not the same as mono
by Tom Goddard 27 May '20

27 May '20

Try "camera sbs" and see if shadows look right. If they do look ok, but stereo does not then it will require some debugging with a stereo system that reproduces the problem and I am not able to test that until quarantine is over. Tom > On May 26, 2020, at 10:01 AM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> wrote: > > Thanks. I will check out the versions as they come out. Hopefully this can be fixed. I can try a VR and see what is up with the display if anything. > kas > > > Kenneth A. Satyshur, M.S., Ph.D. > Senior Scientist, > Department of Bacteriology: College of Ag and Life Sciences; > Departments of Bio Molecular Chemistry, > Neuroscience, Oncology, and Carbone Cancer Center: > School of Medicine and Public Health; > and the School of Pharmacy > University of Wisconsin-Madison > Madison, Wisconsin, 53706 > 608-215-5207 > From: Tom Goddard <goddard(a)sonic.net> > Sent: Tuesday, May 26, 2020 11:48 AM > To: Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] 3D stereo lighting is not the same as mono > > I made a bug report for this > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315> > > I am not able to test stereo, don't have a computer that can do it. For me other two eye modes like VR and SBS (side-by-side) have correct shadows. The problem may be a graphics driver bug effecting shadow calculation. Or it might be a bug in ChimeraX in how OpenGL quad-buffering are used. > > Tom > > >> On May 23, 2020, at 4:39 PM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu <mailto:kenneth.satyshur@wisc.edu>> wrote: >> >> I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with >> >> camera stereo >> >> the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. >> But a Great improvement in rendering of images. >> thanks >> kas >> p.s. old chimera does stereo very well on my system >> Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux >> >> >> Kenneth A. Satyshur, M.S., Ph.D. >> Senior Scientist, >> Department of Bacteriology: College of Ag and Life Sciences; >> Departments of Bio Molecular Chemistry, >> Neuroscience, Oncology, and Carbone Cancer Center: >> School of Medicine and Public Health; >> and the School of Pharmacy >> University of Wisconsin-Madison >> Madison, Wisconsin, 53706 >> 608-215-5207 >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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3D stereo lighting is not the same as mono
by Kenneth Satyshur 26 May '20

26 May '20

I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with camera stereo the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. But a Great improvement in rendering of images. thanks kas p.s. old chimera does stereo very well on my system Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences; Departments of Bio Molecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center: School of Medicine and Public Health; and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207

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Recreating views
by Martin Montgomery 22 May '20

22 May '20

Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM Martin G Montgomery Senior Scientist ATP Synthase Group MRC Mitochondrial Biology Unit University of Cambridge The Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY www.mrc-mbu.cam.ac.uk <http://www.mrc-mbu.cam.ac.uk/>

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Save/restore scene?
by Oliver Clarke 20 May '20

20 May '20

Hi ChimeraX-ers, Is there currently an equivalent of the "scene" command from Chimera? It was super helpful to be able to quickly switch between different (and often complex) representations of a molecule. I know the view command for saving and restoring orientations, and the "name" command for saving selections, but I can't find an equivalent of scene. I'm guessing it's not yet implemented, but count me as one vote for porting it over after 1.0 is out the door, it was super helpful in Chimera! Cheers Oli

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Feature suggestion - show color code in picker?
by Oliver Clarke 20 May '20

20 May '20

Hi, I love the color editor in ChimeraX, it is much nicer than the one in Chimera and is super useful! One minor suggestion - would it be possible to add a dynamically updated label showing in the editor the current color code? This sometimes shows up in the log but not always, and it is useful to have easily copy-able for use in scripts and aliases. Cheers Oli

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Cartoon smooth loops chimX
by Dominik Hrebík 19 May '20

19 May '20

Hi all! Is there any possibility to smooth loops in cartoon representation in ChimeraX? I can't find it in the user guide. Something similar to pymol's cartoon_smooth_loops,1: https://pymolwiki.org/index.php/Cartoon_smooth_loops Best, Dominik -- ################################## Dominik Hrebik Laboratory of Structural Virology CEITEC, Masaryk University Kamenice 5 / A35 Brno, 625 00, Czech Republic Phone: +420 549 49 7764 <%2B420%20549%2049%207756> ##################################

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Focus in ChimeraX
by Luca Pellegrini 18 May '20

18 May '20

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

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Turntable rotation
by Scott, Brandon L. 16 May '20

16 May '20

I would like to create an animation where the camera is spun around at a constant azimuthal angle so the object appears to spin on a tabletop. Currently, when I use roll, when it spins to the backside I see underneath the model rather than remaining on top. Any help is greatly appreciated. -Brandon ____________________ Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor SDSMT, Nanoscience and Nanoengineering

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Re: [chimerax-users] transition from Chimera
by Tom Goddard 15 May '20

15 May '20

Hi Jerome, Putting that "open instructions,html" in your startup preferences is a nice way to show an HTML interface that could have links that execute commands in ChimeraX. I had not thought of that use. Tom > On May 15, 2020, at 1:37 AM, MUTTERER Jerome (IBMP) <jerome.mutterer(a)ibmp-cnrs.unistra.fr> wrote: > > Hi Tom, > Thank you very much for your answers. > I didn't try the drag and drop emulation approach, but I confirm the "remotecontrol rest" option at startup works nicely. > I added the following 2 lines to the Favorites>Settings...>Startup tab > > remote rest start port xxxxx > open instructions.html > > and it makes it easy to operate. > Thanks a lot! > > Jerome > > > De: "Tom Goddard" <goddard(a)sonic.net> > À: "MUTTERER Jerome, IBMP" <jerome.mutterer(a)ibmp-cnrs.unistra.fr> > Cc: chimerax-users(a)cgl.ucsf.edu > Envoyé: Mardi 12 Mai 2020 20:14:39 > Objet: Re: [chimerax-users] transition from Chimera > > Hi Jerome, > > We don't have the chimerax --send option to open files in an already running ChimeraX, although we plan on adding it. > > I have two ideas for how to do this in current ChimeraX. One is to use the remotecontrol command to tell ChimeraX to accept commands via http. In ChimeraX I enable this with command > > remote rest start port 58123 > > Then http requests can run commands in ChimeraX. The http url can be entered in a web browser or from a script. From a script you could use curl or wget programs, for example, > > curl http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P… <http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P…>.cif > > You could make ChimeraX alway enable http requests by putting the "remote..." command in ChimeraX Settings/Preferences under the Startup tab "Execute these commands at startup". > > The other idea I have is simpler but did not work in my test. ChimeraX accepts files dragged and dropped on the application. On macOS (and probably Linux and Windows) I should be able to run a shell command that says drop this file on ChimeraX. On Mac the shell command looks like > > % open -a /Applications/ChimeraX.app ~/Downloads/ChimeraX/PDB/1a0m.cif > > That worked for starting ChimeraX and showing the first file. But when I run it again to open a different it merely raised ChimeraX and did not open the new file. That is a bug. I've made a bug report for it. I don't know the equivalent commands on Linux and Windows and whether the would work. > > Tom > > > On May 12, 2020, at 1:50 AM, Jerome Mutterer <jerome.mutterer(a)ibmp-cnrs.unistra.fr <mailto:jerome.mutterer@ibmp-cnrs.unistra.fr>> wrote: > > Dear all, > I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send> > > I see that this is not described here: > https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html <https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html> > > Is that still available somehow in ChimeraX? > Thanks for any input. > Sincerely, > Jerome. > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr/> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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Stuck on one XML-RPC command
by Mungo Carstairs (Staff) 14 May '20

14 May '20

Any XML-RPC fans who can help me with this please? This label command works in the PyMOL command line: label 4zho//A/36/CA 4zho//B/36/CA, "hello world" How do I format an equivalent XML-RPC request? I've tried <methodCall> <methodName>label</methodName> <params> <parameter> <value>4zho//A/36/CA 4zho//B/36/CA</value> </parameter> <parameter> <value>"hello world"</value> </parameter> </params> </methodCall> but get back a fault response XML message with <class 'SyntaxError'>:invalid syntax (<string>, line 1) I have also tried encoding the " as %22, or omitting the quotes, same result. Any ideas please? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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Stereo and VR support
by Gökhan Tolun 14 May '20

14 May '20

Hi, Would it be possible to make the graphics window undockable, too, Like the other ones? This would allow the use of stereo monitors with SBS and tb support, which does not work currently with menus, etc. surrounding the graphics window. Also, will you implement DTI stereo as in Chimera? By the way, if theres a way of making ISOLDE work in VR, thatd be great! Thanks, Gökhan

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pyqtchart
by Anthony James Schaefer 14 May '20

14 May '20

Hello, I'm interesting in using pyqtchart (https://pypi.org/project/PyQtChart/) as an alternative to matplotlib for some plots in my bundle (I like the default style better, it resizes better - small things like that). If I list pyqtchart as a dependency in my bundle_info.xml like ... <Dependencies> <Dependency name="pyqtchart"/> </Dependencies> ... a new version of PyQt5 gets installed in the directory where bundles get installed. The QChart module from pyqtchart gets installed in this new PyQt5 package. I can't use the QChart module because it's not in the PyQt5 that ChimeraX uses. Is there anything I can do with my bundle to get it to install a usable pyqtchart? Thanks, Tony

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wrong version in download
by Christine Gee 13 May '20

13 May '20

Dear ChimeraX I downloaded what was supposed to be chimeraX 0.5 from your site, and 0.1 instead. I have an older mac with an older OS (10.11.6) and would like the last version that was developed for it. Can you please let me know where I can download 0.5? Also does it work with isolde? Regards Christine Dr Christine Gee Research Specialist Kuriyan Lab HHMI/Molecular and Cell Biology/QB3 527 Stanley Hall MC 3220 University of California, Berkeley Berkeley, CA 94720-3220 Lab Phone: 510 643 0164 Cell: 510 230 7891 Email: christinelgee(a)berkeley.edu <mailto:christinelgee@berkeley.edu>

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Manual segmentation in ChimeraX
by Pattana Jaroenlak (Michael) 13 May '20

13 May '20

Hello, I saw the twitter post from ChimeraX on segmentation of EM serial images ( https://twitter.com/ucsfchimerax/status/1260425173238415360?s=12) It was very beautiful. I have serial section EM images. I am wondering that can I do manual segmentation on ChimeraX? Some cellular features on my images can not be picked up by thresholding or watersheding. Thank you PJ -- *Pattana (Michael) Jaroenlak, PhD* Bhabha & Ekiert Labs Skirball Institute of Biomolecular Medicine New York University School of Medicine *Email: pattana.jaroenlak(a)nyulangone.org <pattana.jaroenlak(a)nyumc.org>, p.jaroenlak(a)gmail.com <p.jaroenlak(a)gmail.com>*

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Renaming chain IDs
by Fahrenkamp, Dirk 12 May '20

12 May '20

Hi ChimeraX team. I am happily using chimeraX along with ISOLDE for modelling. Lately, I am running into issues with complexes having too many chains to be handled by the standard .pdb format which is why I am using .cif now. Is there a smooth way/command to rename chain IDs and change _entity.pdbx_description _struct_asym.entity_id accordingly? Thanks! Kind regards, Dirk -- Dr. rer. nat. Dirk Fahrenkamp UKE Hamburg Zentrum für experimentelle Medizin Institut für Struktur- und Systembiologie/ CSSB Centre for Structural Systems Biology c/o Deutsches Elektronen-Synchrotron DESY Notkestraße 85, Building 15 3.OG D-22607 Hamburg Telefon:+49 (0) 40 8998-87657 Dirk.Fahrenkamp(a)cssb-Hamburg.de www.cssb-hamburg.de

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transition from Chimera
by Jerome Mutterer 12 May '20

12 May '20

Dear all, I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send I see that this is not described here: https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html Is that still available somehow in ChimeraX? Thanks for any input. Sincerely, Jerome. -- Jerome Mutterer CNRS - Institut de biologie moléculaire des plantes 12, rue du Général Zimmer 67084 Strasbourg Cedex www.ibmp.cnrs.fr

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Map "Blobs" tool - Generate objects?
by Christophe Leterrier 12 May '20

12 May '20

Hi, I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this? Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

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ChimeraX on Twitter
by Tom Goddard 09 May '20

09 May '20

For ChimeraX news, tips, tricks and special features meet us on Twitter @UCSFChimeraX. https://twitter.com/UCSFChimeraX <https://twitter.com/UCSFChimeraX> Tom, Eric, Elaine, Greg, Conrad, Scooter, Tom -- the UCSF ChimeraX team.

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How to display crystal packing?
by Guillaume Gaullier 08 May '20

08 May '20

Hello, Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do. What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions? It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX). Thank you in advance, Guillaume

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preview ChimeraX 1.0!
by Elaine Meng 07 May '20

07 May '20

The ChimeraX 1.0 (!!) release candidate is now available: <http://www.rbvi.ucsf.edu/chimerax/download.html> Please, please try it out and report any issues that you find, as we plan to make the production release by the end of the month. To report issues, use the ChimeraX menu: Help... Report a Bug <http://www.rbvi.ucsf.edu/chimerax/docs/contact.html> For what's new, see the Change Log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Problems with making movie in chimerax
by Nandish Kumar Khanra 07 May '20

07 May '20

Hello all, I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie. * Aligned two models using matchmaker, mm #1 to #2 pair ss ss false * make morph morph #1,2 frames 100 play false cartesian true * make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this? Thanks, Nandish

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Script to color zone a map according to the underlying model
by Caroline Stone 07 May '20

07 May '20

Dear All, As an exercise in scripting, I am trying to write a script to imitate the appearance a published figure (from Toropova et al 2017). I would like to display a semi-transparent map which has been color zoned to match the underlying model in surface view. ChimeraX does everything in the script apart from the last two commands, in which I color zone the map, and then make it transparent. I don't get any errors in the log to give me a clue what to change. If I omit these last two commands from the script and then make them manually from the command line after the script is finished, it works. Is there something I can change that would allow me to include the final two commands in the script? Any pointers would be much appreciated. # ChimeraX script to imitate dynein 2 tail Toropova et al 2017 figure style # Adds custom colours to the ChimeraX session # Open model and set camera view and model rotation open 6RLB windowsize 775 775 view matrix camera -0.30533,0.56038,0.76991,623.53,0.82837,-0.24247,0.50499,467.83,0.46967,0.79195,-0.39016,-7.3434 models #1,1,0,0,0,0,1,0,0,0,0,1,0 # Work with model representation surface #1 set bgColor white lighting soft graphics silhouettes true # Define custom colours color name midblue #6b80b5 color name midgreen #a0c497 color name midyellow #f9ef87 color name midtomato #f97054 color name midmagenta #a4449b # Recolour model using custom colours defined above select #1/A; color sel midblue select #1/B; color sel skyblue select #1/C; color sel midtomato select #1/D; color sel midmagenta select #1/E/F; color sel midgreen select #1/G/H; color sel lightpink select #1/I-N; color sel midyellow select clear # Open map and modify color and transparency open emdb:4918 volume #2 step 1 volume #2 level 0.0172 surface dust #2 size 10 color zone #2 near #1 distance 15 volume #2 transparency 0.75 Best wishes, Caroline

3 3

Silhouettes cause fill
by Daniel Asarnow 06 May '20

06 May '20

Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: [image: image.png] I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1. Thanks and best, -da

4 9

Re: [chimerax-users] Chimera X -showing electrostatic potential
by Elaine Meng 06 May '20

06 May '20

Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so far... I hope you are well too. To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#es…> After you generate the map (e.g. a .dx file, .phi file, or .cube file) <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> ... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> If you open a .cube file it will automatically show as isosurfaces. However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 5, 2020, at 7:14 PM, Yi Shi <yi.shi(a)pitt.edu> wrote: > > Dear Elaine, > > Hope this finds you, your family and colleagues safe and well. > > We have a question about Chimera X software that you and your colleagues developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this? > > BTW, the software that you developed was amazing that we really enjoy it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work! > > Thanks in advance. > Yi > > Yi Shi Ph.D. > Assistant Professor > Department of Cell Biology > Program for Integrative Systems Biology > Pitt/ CMU Program in Computational Biology > University of Pittsburgh School of Medicine > BST3 9049 > 3500 5th Avenue > Pittsburgh PA 15213 > 412-383-3242 (office) > 412-383-3243 (lab) > www.shi-lab.org

2 3

Scroll threshold step size
by Daniel Asarnow 04 May '20

04 May '20

Hi, Is it possible to adjust the step size when using alt + scrollwheel to change the contour level? I'd like to make it coarser for RSI reasons. Thanks, -da

3 6

ubuntu 20.04
by Hua tiger 03 May '20

03 May '20

Please create a download and install package for ubuntu 20.04 Thank you very much. John

2 3

Chimera-Animation equivalent utility/command
by Ray Y.-R. Wang 01 May '20

01 May '20

Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray

2 5

Missing segments
by Daniel Asarnow 01 May '20

01 May '20

Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug? Thanks and best, -da

5 7

morph movie with secondary structure and dssp
by Joel Meyerson 30 Apr '20

30 Apr '20

Hi, I am making a morph between two PDB models representing two states of the same protein, and the overall secondary structure does not change much between the models. However, there is a region where the secondary structure does change. I would like to capture the secondary structure change in the morph and have a couple questions. 1. It seems the morph uses the secondary structure from PDB #1. Is there a way to use the two different secondary structure headers from the two PDBs to define the secondary structure endpoints on the morph? 2. If the above is not possible, is there a way to restrict DSSP to update only the region of interest (i.e. a residue range), and not change secondary structure throughout the molecule? Thanks, Joel

2 2

addh and phenix
by Daniel Asarnow 24 Apr '20

24 Apr '20

Hi, Seems like with NAG glycans the addh result is incompatible with phenix real space refinement. It's easy enough to fix by deleting HD2 - the offending hydrogen - manually. I was wondering if anyone had an opinion about this, before I report a phenix bug. Error looks like: Number of atoms with unknown nonbonded energy type symbols: 5 "ATOM 2629 HD2 ASN A 362 .*. H " (4 more similar lines). Best, -da

3 2

How to hide dashed lines?
by Steve Chou 24 Apr '20

24 Apr '20

Dear ChimeraX developers and users, I see a dashed line between an ion and a side chain when I display the side chain. Is there a way to hide the dashed line, either in command line or GUI? How to select all the atoms in residues (e.g., /A:10-100) except n, c, and o atoms? Many thanks, Steve -- Steve Chou

2 1

displaying ribbon and tube simultaneously
by Joel Meyerson 23 Apr '20

23 Apr '20

Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles? Thanks, Joel

3 5

Molecular Docking problem
by Estela Fernandes e Silva 23 Apr '20

23 Apr '20

Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela

2 2

deleting sidechain in ChimeraX
by Joel Meyerson 22 Apr '20

22 Apr '20

Hi, What is the command or sequence of commands which can be used to delete the sidechain on an amino acid or range of amino acids? I reviewed the ChimeraX atom spec page but could not find a way to do this. Thanks, Joel

2 2

Problem with showing 4 Fe-4S in pdb with chimerax
by Meinan Lyu 22 Apr '20

22 Apr '20

Dear chimerax-users(a)cgl.ucsf.edu, There is a 4 Fe-S in my structure, it shows a little bit funny when I open it with chimerax. It should only have links between Fe and S, but between 2Fe shows a link line two. Do you know how to show it normally like in pymol, or remove the links between 2Fe? I really want to draw some figures in chimerax. The attached are 4 Fe-S shown in chimrax,also shown in pymol. PDB id 2WDQ is also attached, which 4 Fe-S is in /B,F,J:303. Thanks very much. Be safe and Best, Meinan Postdoc from CWRU

2 2

shape tool in ChimeraX
by Joel Meyerson 20 Apr '20

20 Apr '20

Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel

3 4

Re: [chimerax-users] [EXT] Re: passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Hi Eric, thanks for your fast help, works now as expected! Philipp Von: Eric Pettersen <pett(a)cgl.ucsf.edu> Gesendet: Mittwoch, 15. April 2020 22:19 An: Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [chimerax-users] passing arguments to python scripts with command runscript Hi Philipp, In ChimeraX, the arguments will be in sys.argv — namely sys.argv[1:] since sys.argv[0] will be the name of your script file. --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 15, 2020, at 12:47 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de <mailto:philipp.milkereit@vkl.uni-regensburg.de> > wrote: Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp _______________________________________________ ChimeraX-users mailing list <mailto:ChimeraX-users@cgl.ucsf.edu> ChimeraX-users(a)cgl.ucsf.edu Manage subscription: <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

1 0

passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp

2 1

syntax on marker and marker link placement
by Joel Meyerson 12 Apr '20

12 Apr '20

Hi, I have a question about marker and marker link syntax. Suppose model #1 has chains A and B, and that chains A and B form a homodimer where each subunit has the same residue numbering. I would like to place a marker at the midpoint between alpha-carbons of position 10 on A and 10 on B. In turn, I'd like another marker at the midpoint between position 20 on each of the two subunits. I would then like to draw a linker between the two markers. I would expect the following syntax to work, but I get an error. marker #2 #1/a,b:10@CA color yellow radius 1 marker #2 #1/a,b:20@CA color yellow radius 1 marker link #2:1,2 color yellow radius 0.5 Gives the error: Missing or invalid "position" argument: Expected 3 floats or object specifier Any suggestions on how to fix the syntax, or is there an alternative approach? Thanks, Joel

2 4

Move Z plane backside
by Aritz Roa Eguiara 09 Apr '20

09 Apr '20

Dear ChimeraX team, I would like to ask if there is any command to move the Z plane but not the front, but the back one, while recording a movie. I am familiar with clipping, however when recording a movie it directly appears, is there any way to do the same move z but for the far plane? Thank you in advance and happy Easter, Aritz

2 1

How to do repetitive task using Python or command line in ChimeraX?
by 이서원 09 Apr '20

09 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as many as the number of the variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (I didn't understand how to import experimental API) Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

3 3

How to do repetitive task using Python or command line in ChimeraX?
by 이서원 09 Apr '20

09 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as there are variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (Experimental API Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

1 0

silhouette scaling and image dimension
by Joel Meyerson 09 Apr '20

09 Apr '20

Hi, I noticed that when I save images in ChimeraX with silhouettes on, the apparent width of the silhouette in the output image seems to scale inversely with the image dimensions. For example, these three commands give slightly different silhouette thicknesses. Images attached. save ~/Desktop/image1.png width 500 height 500 save ~/Desktop/image2.png width 1000 height 1000 save ~/Desktop/image3.png width 2000 height 2000 Is there a way to have a fixed silhouette thickness in output images? I'd also be interested to know why this happens. Thanks, Joel

2 2

Making New Bonds between Protein & Ligand
by Gupta, Arun 08 Apr '20

08 Apr '20

Hi I followed similar " marker link " trick proposed by Tom for making new bonds between a selection of Serine residue of protein molecule with hydroxy group functionality of ligand molecule typing the below mentioned command in ChimeraX command line . marker link #1:54@OG #2:PNS@HOP1@SG radius 0.2 However, I am repeatedly getting following error. " TypeError: Cannot bond atoms in different molecules " Can you plz suggest the correct command or alternative way for making new bond between Protein & ligand molecules. Thanks Arun

2 1

Making new bonds
by Mutum YAikhombA 07 Apr '20

07 Apr '20

Hi I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.htm… <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.htm…>. Could you please help? Thanks Yaikhomba

5 4

cartoon highlight color?
by Joel Meyerson 07 Apr '20

07 Apr '20

Hi, Is there a way to customize the highlight color of helices and strands? For example, here is how it appears in Pymol. https://pymolwiki.org/index.php/Cartoon_highlight_color Thanks, Joel

2 2

cxc script does not execute 'surface dust' command
by Joel Meyerson 07 Apr '20

07 Apr '20

Hi, I am observing inconsistent behavior in the ‘surface dust’ command. When I launch ChimeraX and execute the following commands one-by-one at the command line everything works as expected. However, if I place the commands in a cxc script, then double click the script ChimeraX launches and the script executes, but the ‘surface dust’ command does not hide the dust. In addition, within that same session I can then enter the ‘surface dust’ command manually and it works as expected. I’m running ChimeraX Daily 0.93 (2020-04-04) on Mac OS 10.15.1. Do you know why the command is not working inside a script? close all open map.mrc turn x 90 volume erase #1 center 175,160,314 radius 100 outside true surface dust #2 size 40 Thanks for the help. Joel

2 3

Command "mlp"
by Cosmin Stefan Butnarasu 06 Apr '20

06 Apr '20

Hello, Hope to find you doing well. I am a PhD student in Pharmaceutical and Biomolecular Sciences and I am writing this email because I would like to better understand the mlp command. First of all, I have to say that I am a very novice on ChimeraX, I discovered this software basically few days ago, so I will write concepts that maybe are not properly correct. I would like to calculate the surface hydrophobicity of a protein. I saw that the mlp command graphically displays the molecular lipophilicity potential, which I suppose is somehow close to the surface hydrophobicity. However, when mlp command is compute, in the Log panel are shown three values, a minimum, a mean and a maximum, which I have not completely understood what they are for (see the picture attached). I searched on ChimeraX manual and I found that the SES surface could stand for “solvent-excluded surface” but I’am not sure about this. If so, could the mean SES value be a measure of the surface hydrophobicity of the protein? If not, can you suggest me a method to obtain not only a graphical display but also a value of the overall molecular lipophilicity potential? Thank you in advance! Cosmin Stefan Butnarasu ********************************************************* Cosmin Stefan Butnarasu, PhD Student Department of Molecular Biotechnology and Health Sciences University of Torino Via Gioacchino Quarello 15, 10135 email: cosminstefan.butnarasu(a)unito.it *********************************************************

2 3

Questions about ChimeraX
by Yuhua Fang 06 Apr '20

06 Apr '20

Hi Recently I transferred to ChimeraX from the old version. I found: 1. Some SMILE strings copied directly from ChemDraw cannot be recognized by ChimeraX, such as O=C1NC2=C(/C1=C3NC4=CC=CC=C4C/3=C\O)C=CC(Br)=C2 2. Correct me if I am wrong but ChimeraX seems not able to do molecule docking/ligand minimization like the old version, right? Thank you Joshua Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

3 2

Show map only around certain selection
by Karim Rafie 02 Apr '20

02 Apr '20

Dear all, I was wondering how to show part of a map only surrounding certain residues, i.e. I have coordinates for a multiple-chain PDB but I only want to show the electron density surrounding one chain. Any help would be greatly appreciated. Best, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden

2 2

ChimeraX equivalent to "Chimera web data"?
by Ben Webb 01 Apr '20

01 Apr '20

We have a number of web services and tools that generate web data (*.chimerax) files for legacy Chimera. (Typically they load in a PDB file and an alignment and apply some sort of custom view.) What would the equivalent be for ChimeraX? Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

4 9

bundle_info.xml API changes
by Eric Pettersen 01 Apr '20

01 Apr '20

Any non-developers feel free to skip this message. Even for developers, unless you are writing a toolshed bundle that uses the DataFormat, Open, Save, and/or Fetch tags in the bundle’s bundle_info.xml file, you could skip this message. For the two of you that are left, in anticipation of the the ChimeraX 1.0 release sometime this year we are changing some APIs we are unhappy with. Namely, the tags in the in bundle_info.xml that I mentioned in the previous paragraph. As they stand, they are not easily extensible and it is not obvious without looking at the documentation what the various fields do. On top of that, it is difficult to take the information in those tags and present interfaces for options in ChimeraX’s Open/Save file dialogs. Also, there is nothing preventing keywords added to the open command by one bundle from conflicting with keywords added by another bundle. We will be migrating those tags to use bundle_info’s Manager/Provider architecture (described here <https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/bundle_info.html>). Instead of fixed fields, you have keyword/value pairs, which is slightly more self-documenting. Also, a manager can ask a provider for various things, so in one case the manager can provide a partially processed “open” command along with the “rest of line” for the provider to handle its options, if any, and actually open the file, whereas in another the manager can ask for a widget containing options to show in an open or save dialog. In brief, the change allows us to solve some issues that looked pretty intractable with the old scheme. The exact details of the managers and providers supporting these functions are not detailed in that link (just the generic mechanism), but details will be added as implementations are completed. For convenience, there will some period of time when both the old scheme and new scheme will both work, but we anticipate dropping the old scheme before the 1.0 release. —Eric Eric Pettersen UCSF Computer Graphics Lab

2 4

Keep coordinates and radii of atoms
by Aritz Roa Eguiara 31 Mar '20

31 Mar '20

Dear ChimeraX Team, I am trying to represent a channels in ChimeraX. The output of Mole 2.5 is a .py for Chimera and I am trying to manually transfer to ChimeraX. Is there any easy way to do that? I would need that the coordinates and the radii of each atom is respected, but if I save it from Chimera in PDB the radii is not saved and saving the different atoms manually and then adding a script to give the the proper radius is extremely time consuming. Any suggestion? All the best, Aritz

2 1

upgrading ChimeraX Toolshed
by Greg Couch 30 Mar '20

30 Mar '20

We're modernizing the ChimeraX Toolshed code base. There is a chance that it won't be accessible for day or two. And there's a chance it will be fixed in the next hour. :-) -- Greg

1 0

volume onesmask usage question
by Alexis Rohou 30 Mar '20

30 Mar '20

Hi there, I was trying to use "volume onesmask" to go quickly from a dusted surface of a low-pass-filtered volume to a mask volume with the same dimensions, spacing, etc. as the input map. I thought "fullmap" might be a way to achieve this (the doc says "The remaining options are the same as described for volume mask"), but I don't think that option actually works with "volume onesmask": volume onesmask #3 fullmap true *Expected a keyword* Is there a "onesmask"-like operation or set of options that creates an output volume that's on the same grid as the input volume? Thanks, Alexis

3 7

ToolInstance context menu displaying help
by Anthony James Schaefer 27 Mar '20

27 Mar '20

Hello, can tools' "Help" option in the context menu be changed to use `ToolInstance.display_help` instead of running the `help` command? I'd like to keep most of my documentation on GitHub. The `help` command cannot open URLs, so I thought I'd overwrite my tools' `display_help` methods to use `open` instead. However, I discovered this method isn't used anywhere. I've tried changing `_show_context_menu` in chimerax.ui.gui (around line 2087) to `help_action.triggered.connect(ti.display_help)`. It seems to behave the same for all built-in tools. I understand there might be reasons to not do this (e.g. users might not be able to connect to the internet). I'd like to keep stuff on GitHub because I can make a page on a GitHub wiki page faster than an HTML doc. Regardless of how tools' help pages get shown, I'd like to have examples of what my bundle can do on the GitHub wiki. To that end, my GitHub wiki could serve a dual purpose: a showcase and documentation. Best, Tony

3 4

Coloring of atomic model surfaces
by Rasmus Kock Flygaard 27 Mar '20

27 Mar '20

Dear ChimeraX developers, I have a question regarding coloring of a surface representation of an atomic model. I open the pdb file and turn on surface representation with the command, surface #1 resolution 6 This works just fine. Then I color the surface by command, color #1 skyblue This also works fine. And then I want to color the surface of only a range of residues using the command, color #1:50-86 indigo target s But nothing happens. The reply log says that 1 surface was colored but no color changes is seen in the surface representation. Am I missing something in the color command for surfaces?? Any help is appreciated! Best, Rasmus Kock Flygaard

2 1

addAtom
by Aritz Roa Eguiara 26 Mar '20

26 Mar '20

Dear ChimeraX team, Maybe it is a silly question but I have been trying to add atoms on ChimeraX but I have not found the way, is there any possibility? I need to plot a channel on my protein but I do not manage to do it without that. Thank you in advance. Best wishes, Aritz

2 2

Loss of image quality
by Lucas Tafur 26 Mar '20

26 Mar '20

Hi, I hope everything is going well considering the circumstances. I've been enjoying ChimeraX but have now encountered an annoying issue. Without any apparent reason, the quality of my rendered images becomes very bad, eventhough I'm using the same command and sampling. I've been saving using the following command: save C:\Users\XXXXX.png transparentBackground true supersample 3 It always worked fine until this week (actually, two days ago the quality was still good). Suddenly it started getting bad. I'm using version 0.93. Any help would be appreciated. Best, Lucas

2 1

NMR CSPs
by Bohg, Claudia 25 Mar '20

25 Mar '20

Hey, is it somehow possible to use this attribute in Chimera X? http://www.cgl.ucsf.edu/chimera/data/nmrcolor-nov2017/nmrcolor.html Best, Claudia

2 3

ChimeraX VTK Export
by Angelos Angelopoulos 19 Mar '20

19 Mar '20

Hello, It would be absolutely great if ChimeraX supported exporting to a VTK file like Chimera did. Are there any plans to port the VTK export functionality from Chimera to ChimeraX? If not, please consider doing it. Thank you very much. Sincerely, Angelos Angelopoulos

2 2

Re: [chimerax-users] Making movies and fitting structures into cryoEM
by Elaine Meng 13 Mar '20

13 Mar '20

Dear Madhan, My previous message already explained how you would move only one model in ChimeraX (you have to select part of it with Ctrl-click and then use the mouse mode "translate selected models" etc.). For example clicking the "translate selected models" icon in the Right Mouse toolbar assigns this mode to the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac). See here for which Right Mouse icons go with which functions: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> It sounds like even when you are moving everything together, you don't know how to translate models (up, down, left right) in either program. In Chimera, the default for translation is middle mouse button, or touchpad + option key on Mac (the key may be different on WIndows, just try the ones to the left of the space bar to see which one works). See the Mouse Preferences (menu Favorites... Preferences, change to category: Mouse) for button assignments: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse> See also "using touchpad or 1-button or 2-button mouse" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#2button> In ChimeraX, use command "mousemode" if you want to change assignments. The "mousemode" manpage linked below also shows a table of the default assignments, e.g. translation is middle mouse button, or Mac trackpad + Alt (or 3-finger drag if multitouch enabled), or Windows trackpad + Ctrl-Alt. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> I hope this helps, Elaine > On Mar 13, 2020, at 11:28 AM, Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> wrote: > > Dear Elaine > > Thank you again. > > In Chimera - am able to lock one model by unchecking the "A" box in the Model Panel - in the particular example am working with, its the Cryo-EM density map - the other model is the atomic model from the crystal structure (PDB file) - am not able to move the atomic model into the Cryo-EM density model. When I use the mouse, all am able to do is rotate the second (atomic) model at the same place - am not able to move it from its location on the screen. > > In ChimeraX - its the same problem and since it does not have the model planel, both models are moving at the same time - the commands are a bit confusing as well > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Friday, March 13, 2020 10:07 AM > To: Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Making movies and fitting structures into cryoEM > > Dear Madhan, > I don't understand "not able to lock" in ChimeraX or "not able to move" in Chimera. > > In Chimera, you can control whether each model is hand-movable or not by checking/unchecking the "A" (activated) boxes in the Model Panel, as discussed here: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> > > Show the Model Panel from the Chimera Favorites menu. > > By hand you can then move the atomic model to roughly the correct place in the map before optimizing the fit with Fit in Map. > > The ChimeraX tool Fit in Map is basically the same as the Chimera tool. However, in ChimeraX, the way to move just one model is to select some part of it (Ctrl-click) and then use the mouse mode "move selected models" as discussed in this earlier post: > <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html> > > Also if you additionally press Shift, that mode switches between rotate and translate. > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Mar 12, 2020, at 6:23 PM, Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> wrote: > > > > Dear Elaine > > > > Thank you - all those tips were useful. > > > > With ChimeraX, am not able to lock the Cryo-EM density map and then use the crystal structure to fit into it. > > > > Whereas Chimera allows me to do so - however am not able to move the crystal structure to superimpose on the CryoEM density to do the 'Fit in Map' > > > > is it something am not doing right? I follow these instructions - https://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#… > > > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > > Sent: Wednesday, March 11, 2020 5:22 PM > > To: Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> > > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > > Subject: Re: [chimerax-users] Making movies and fitting structures into cryoEM > > > > Dear Madhan, > > Although ChimeraX doesn't yet have a movie-making dialog (GUI), you can make movies with ChimeraX command scripts. In a command script (plain text file named ending in .cxc), the "movie" command does recording and creating a movie file, whereas other commands (show/hide, color, turn, 2dlabel, etc.) can be used to control display, motions, and labeling... whatever you want to happen during the movie. Simply opening the .cxc file runs the commands. > > > > You can change volume thresholds with the "volume" command "level" option, for example: > > > > volume #1 level 0.08 > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> > > > > To gradually change the threshold over multiple display frames, you can combine the "volume" command with the "perframe" command, for example: > > > > perframe "volume #2 level $1" range 0.1,0.3 frames 120; wait 120 > > > > (those should be plain text quotation marks, although the e-mail display may change them to fancy quotation marks) > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> > > > > See ChimeraX "making movies" page and links therein: > > <http://rbvi.ucsf.edu/chimerax/docs/user/movies.html> > > > > ...including movie-making tutorials: > > <http://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html> > > <http://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html> > > > > See also general information on ChimeraX command files: > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> > > > > For your other question, if you are asking how to fit an atomic structure into a map, see the "Fit in Map" tool and/or "fitmap" command: > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html> > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html> > > > > Or to compare one atomic structure to another atomic structure, you can superimpose them with the "matchmaker" command: > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> > > > > Chimera has a Matchmaker GUI, but ChimeraX does not have the GUI yet, only the command. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > >> Begin forwarded message: > > >> > > >> From: "Tirumalai, Madhan R" > > >> Subject: ChimeraX > > >> Date: March 11, 2020 at 1:10:41 PM PDT > > >> To: "goddard(a)cgl.ucsf.edu" <goddard(a)cgl.ucsf.edu> > > >> > > >> Dear Dr. Goddard > > >> > > >> Warm Greetings! > > >> > > >> We have been using ChimeraX to look at mrc files. > > >> > > >> While I am able to use the "Spin movie" option, am not able to use the make movie option, which I could with the Chimera version. > > >> > > >> I would much appreciate if you could kindly let me know how: > > >> > > >> I can use the movie making option to make movies using different images with increasing/ decreasing thresholds (Volume Viewer)? > > >> > > >> Since am not familiar with docking programs, I would like to know how can one a related crystal structure into a new Cryo-EM structure to show the differences between the crystal structure and the Cryo-Em? > > >> > > >> Thanks > > >> Madhan

1 0

VR movie
by Matthias Wolf 13 Mar '20

13 Mar '20

Hi Tom, I really liked your CoV movie https://www.youtube.com/watch?v=dKNbRRRFhqY&feature=youtu.be It’s a new way of storytelling. Although we have used chimeraX in the lab with a Vive and Vive pro for about 2 years, it’s usually one person at a time, with a dark background. But your way opens up interactive VR to a larger audience (even if they don’t get to enjoy the stereoscopic 3D). And it’s cool. I have some questions: 1. How did you overlay the chimera viewport sync’d with the life camera feed showing yourself? Did you use a frame grabber on a different PC to capture the full-screen chimeraX VR viewport while simultaneously recording the camera video stream, e.g. using Adobe Premiere? 2. How did you control flipping out the outer spike domain with your hand controller? I guess you assigned control of a torsional angle in the atomic model to a mouse mode? 3. Did you enable the headset cameras to orient yourself in the room? Thanks for keeping improving chimeraX and VR! Matthias

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Making movies and fitting structures into cryoEM
by Tom Goddard 13 Mar '20

13 Mar '20

> Begin forwarded message: > > From: "Tirumalai, Madhan R" > Subject: ChimeraX > Date: March 11, 2020 at 1:10:41 PM PDT > To: "goddard(a)cgl.ucsf.edu" <goddard(a)cgl.ucsf.edu> > > Dear Dr. Goddard > > Warm Greetings! > > We have been using ChimeraX to look at mrc files. > > While I am able to use the "Spin movie" option, am not able to use the make movie option, which I could with the Chimera version. > > I would much appreciate if you could kindly let me know how: > > I can use the movie making option to make movies using different images with increasing/ decreasing thresholds (Volume Viewer)? > > Since am not familiar with docking programs, I would like to know how can one a related crystal structure into a new Cryo-EM structure to show the differences between the crystal structure and the Cryo-Em? > > Thanks > Madhan > > > Madhan R Tirumalai, Ph.D., > Houston Science Center, #421 > Dept Biology & Biochemistry, University of Houston, 3455, Cullen Blvd, Houston, TX,77204-5001, USA. > Contact nos: 713-632-5463 (Cell); 713-743-8365 (office); 713-743-8351 (Fax) > > email: mrtirum2(a)central.uh.edu <mailto:mrtirum2@central.uh.edu>, madhanrt(a)gmail.com <mailto:madhanrt@gmail.com> > > ORCID link: http://orcid.org/0000-0002-5999-333X <http://orcid.org/0000-0002-5999-333X>

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Re: [chimerax-users] HP Reverb headset
by Tom Goddard 13 Mar '20

13 Mar '20

Hi Shingo, I think Oculus Rift S is the best choice for ChimeraX VR. Unfortunately all the good VR headsets are sold out apparently because of production delays in China the last few months. So you will have to be patient. I think it is worth waiting instead of getting a headset that will not function well. Tom > On Mar 12, 2020, at 5:47 PM, 永野真吾 <snagano(a)tottori-u.ac.jp> wrote: > > Tom, > > Thank you for the very quick response and useful information. I will get Oculus Rift S. > > All the best, > > Shingo > > > > 2020年3月13日(金) 4:01 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Shingo, > > I have not used the HP Reverb VR headset but I have used another Windows Mixed Reality headset, the Samsung Odyssey, which worked fine in ChimeraX. ChimeraX just uses the Windows Mixed Reality runtime through SteamVR so I expect any Windows Mixed Reality headset will work. That said, the reviews on the HP Reverb are poorer than other headsets > > https://www.amazon.com/HP-Reverb-Virtual-Reality-Headset/dp/B07R768KJP <https://www.amazon.com/HP-Reverb-Virtual-Reality-Headset/dp/B07R768KJP> > > I would recommend Oculus Rift S which I have used extensively with ChimeraX. I also have used Vive Pro, Vive, Oculus Rift, and all those work well. > > Tom > > > On Mar 12, 2020, at 3:25 AM, 永野真吾 <snagano(a)tottori-u.ac.jp <mailto:snagano@tottori-u.ac.jp>> wrote: > > > > Hi all, > > > > Has anyone used HP Reverb headset for virtual reality on ChimeraX? > > That headset works fine? > > > > Any comments are welcome. > > > > Best, > > > > Shingo Nagano > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > > Manage subscription: > > http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> > > >

1 0

flatten a cryoEM map
by Hongtao Zhu 12 Mar '20

12 Mar '20

Hi there, Could you show me how to flatten a cryoEM map in chimera just like the attachment? My map has several subunits but with C1 symmetry. Thanks, Hongtao

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ChimeraX does not start after installation
by Lewandowski, Jozef 12 Mar '20

12 Mar '20

Hi, I am trying to get ChimeraX on a Windows 10 installation on a workstation with 4 GPUs (RTX 2080Ti). The program installs just fine but when I start it, it shows the splash screen up to Loading main interface and then quits. I have tried both with the 0.92 release and the daily_build. Any chance you could help with with getting it to work? Browsing archives I learned that this may be down to some incompatibilities with drivers. The onboard graphics is ASPEED Graphics Family with driver version 9.0.10.102 The four Nvidia GeForce RTX2080Ti have driver 26.21.14.4219 installed (I updated to the latest drivers hoping it fixes it - it doesn't). Any ideas or suggestions? Thanks, Józef

2 1

HP Reverb headset
by 永野真吾 12 Mar '20

12 Mar '20

Hi all, Has anyone used HP Reverb headset for virtual reality on ChimeraX? That headset works fine? Any comments are welcome. Best, Shingo Nagano

2 1

Error opening sequence viewer
by Y. Mutum 12 Mar '20

12 Mar '20

Hi I am working with ISOLDE to build my model using ChimeraX interface. There I had added an deleted a few sequences in chain a. This was done while the sequence viewer was closed. Now, when I try to view the sequence by ' sequence chain #1/a', I am getting this error (attached as screenshot) Could you please help? I hope I don't have to start from the begining. Thanks Yaikhomba

3 2

How to save the ChimeraX startup settings?
by Steve Chou 11 Mar '20

11 Mar '20

Dear ChimeraX team, It seems that if the startup window size settings ( display window size, log window width) are different, I get different views after I run the same script, which has a lot of operations, like “move”, “turn”. How to save the startup settings and load them back or is there a startup settings file saved somewhere? Many thanks, Steve Chou -- Steve Chou

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Re: [chimerax-users] pseudobond between atom and center of a ring
by Elaine Meng 10 Mar '20

10 Mar '20

Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form: /a:1@c3' /a:1@n3 rgba(20,90,90,70) However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent: /a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html> Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou(a)gmail.com> wrote: > > Thanks Elaine! > > Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks! > > Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck. > > Thanks again for the help. > > Cheers, > Alexis > > On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Here is the more detailed description of pseudobond file format: > > <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>

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sessions vs. logging
by Eric Pettersen 09 Mar '20

09 Mar '20

Hi all, As of tomorrow’s daily build, restoring a session will by default clear the log and restore the contents of the log from the session, hidden under a dated disclosure triangle. There is a preference in the “Log” preferences category to not clear the log (but still add the old log under a disclosure triangle). If you are a big fan of the current behavior and don’t want the old log to be added at all, I can add an option for that. If you are, feel free to speak up (but maybe try out the new behavior first?). These dated disclosure triangles “nest”, in that if you do some work and save a session, then later restore that session and do more work and save a second session, when you restore that second session you will see one disclosure triangle that shows the second set of work you did — but at the top of that second set of work will be a disclosure triangle that can be opened to show the first set of work you did. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimerax-users] not showing non-traced amino acids in sequence view after splitting a molecule
by Tom Goddard 06 Mar '20

06 Mar '20

Hi Marta, Thanks for the explanation of why you use split. Suppose Model Panel showed each chain, and you deleted all the unwanted chains. Would that work as well as split? Definitely split should preserve the sequence information for missing structure, so we appreciate you bringing that to our attention. Tom > On Mar 6, 2020, at 3:04 AM, Marta Perez Illana <marta.perez(a)cnb.csic.es> wrote: > > > Thanks a lot for the ideas and opening the topic, that was absolutely great and appreciated. I just wanted to make sure that I was not messing around myself with the splitting+sequence thing. > > Ideally I wouldn't use the split as you both suggested... However, I frequently use the match maker with several homology proteins coming from big viruses with lots of proteins... and having less proteins in the session really helps me not to get confused and focus and switching on and of every protein at each time... So I am afraid that I really adore the split command. > > Having the full sequence on the other side helps me out to compare the homology proteins and see which areas are traced in one protein but not in the other (or parts of the protein that are subjected to protease fragmentation and not visualized in the structure) , as well as to get full alignments based on structure... > > I am really grateful for all the help and sorry for being a bit picky on the split+sequence... > > Marta > > > >> On 05.03.20 20:56, Tom Goddard wrote: >> Hi Marta, >> >> The sequence for the missing structure should be preserved by the split command but it currently is not being preserved. We have opened a request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2913 >> >> I agree with Elaine, that you should rarely need to use the split command. >> >> Tom >> >> >>> On Mar 2, 2020, at 9:15 AM, Marta Perez Illana wrote: >>> >>> Hi Elaine >>> >>> Thanks a lot for the quick reply! I though that maybe there was a way to keep that info of the non-traced amino acids after doing splitting. >>> >>> I use split because we work with huge molecules, and therefore is really convenient for focusing on a particular chain. And as well for fitting as you mention... I will try the alternatives you proposed! now knowing that making/saving new models implies for sure kind of "loosing that info"... >>> >>> Regards >>> >>> Marta >>> >>> >>>> On 02/03/2020 18:05, Elaine Meng wrote: >>>> Hi Marta, >>>> When you open a structure from PDB or mmCIF format, there is a special part of the file that gives the full sequence of the structure used in the experiment, even if parts of that structure are not visible in the density (and therefore do not have atomic coordinates). This is part of the model information. >>>> >>>> However, “split” makes new models, and it currently loses various kinds of information. I believe this is the case in both Chimera and ChimeraX. After splitting, it must only look at the coordinates to get the sequence. >>>> >>>> My personal opinion is to avoid using “split” unless it is really necessary. >>>> >>>> In Chimera it sometimes helped with molecular surface calculation, but in ChimeraX there is less reason to do it. You can specify chains individually without splitting. The main reason one might split is for separately fitting the chains. However, if having the full sequence is important, you can instead open multiple copies of the original model and just delete the parts of each that you don’t need. >>>> >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>>> On Mar 2, 2020, at 8:30 AM, Marta Perez Illana wrote: >>>>> >>>>> Hi all >>>>> When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure). >>>>> >>>>> Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please? >>>>> >>>>> P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed... >>>>> >>>>> Thank you!!! >>>>> Marta >>> >>> -- >>> Marta Pérez Illana, Ph. D. student >>> Dept. of Macromolecular Structures Lab 15 >>> Centro Nacional de Biotecnología (CNB-CSIC) >>> Darwin, 3 >>> 28049-Madrid (SPAIN) >>> http://wwwuser.cnb.csic.es/~sanmartinlab >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > -- > Marta Pérez Illana, Ph. D. student > Dept. of Macromolecular Structures Lab 15 > Centro Nacional de Biotecnología (CNB-CSIC) > Darwin, 3 > 28049-Madrid (SPAIN) > Email: marta.perez(a)cnb.csic.es > Phone: (0034) 91 585 4508 > http://wwwuser.cnb.csic.es/~sanmartinlab

1 0

pseudobond between atom and center of a ring
by Alexis Rohou 06 Mar '20

06 Mar '20

Hi all, Looking for ideas on how to achieve the following, if possible: I'd like to draw lines to represent favorable ring-ring stacking interactions (lines between the center of two arene rings), ring-ring edge-to-face interactions (between one atom of one ring and the center of the other ring), and between a regular atom (not part of a ring) and the center of an arene ring. So I'm guess what I'm looking for is a way to: 1. compute the center coordinates of a ring 2. place an invisible atom there 3. create a pseudobond between this virtual atom and other atoms/virtual atoms Any suggestions as to how I could achieve this? Cheers, Alexis

3 6

Depth cueing and silhouette
by Aritz Roa Eguiara 05 Mar '20

05 Mar '20

Dear ChimeraX team, I write you to ask about the depth cueing option. I have a structure with the silhouette true option and now I want to change the depth cueing to obtain a slice of the structure but with some of the fog coming from the background. The cartoon color disappear gradually as expected, however the black line of the silhouette is 100% or nothing, is there anything I am doing wrong or is it what I should expect? Is there anyway to obtain also that smooth disappearing of the silhouette? Thank you for your help. All the best, Aritz

4 6

not showing non-traced amino acids in sequence view after splitting a molecule
by Marta Perez Illana 05 Mar '20

05 Mar '20

Hi all When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure). Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please? P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed... Thank you!!! Marta

3 4

Secondary structure display - pdb and cif
by Tetter Stephan 05 Mar '20

05 Mar '20

Dear ChimeraX users and developers, I am having an issue with secondary structure display. I am real-space refining a set of 120 chains in phenix. Of these, only 10 are unique, the rest is symmetry-related. Thus, I define secondary structure elements for the 10 unique chains only. The output pdb file header contains the secondary structure elements as imposed during refinement. Displaying this pdb file in ChimeraX shows the right secondary structure. The mmcif file instead, whether I use the phenix output or generate it from the pdb myself, displays different, non-sensical structures. Secondary structure is shown in loop regions, and some actual strands and helices not recognized at all. This artifact is only shown for the 10 subunits with secondary structure definitions, the other subunits show no secondary structure at all, thus something is read in, but not correctly, apparently. Any idea what the problem could be? Could the size of the complex be an issue? The attachments show the lines from the two file types concerning secondary structure definitions. Kind regards, Stephan

3 3

"zone" near MULTIPLE residues in ChimeraX
by Steve Chou 03 Mar '20

03 Mar '20

Dear ChimeraX team, I tried to use the zone command to display the atomic details and DENSITY near THREE residues of interest. These three residues are ligands and bind to the same place. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html As the above manual said, the zone command can only display things near ONE residue. Is there a way to work around this? Many thanks, Steve -- Steve Chou

3 3

Bug: selection of atoms by attribute = color
by Pavol Bardy 393791 28 Feb '20

28 Feb '20

Hello, since version 0.91 I am experiencing problems with selecting atoms by color attribute "@@color=color". I am getting an error message "Expected an objects specifier or a keyword". In version 0.90 everything works fine. Other attributes like "bfactor" or "idatm_type" seems to work normally. Kind regards, -- Pavol Bárdy Laboratory of Microbial Molecular Diagnostics Department of Experimental Biology, Masaryk University Kamenice 5 / A25 Brno, 625 00, Czech Republic

2 1

change residues to helix
by Meinan Lyu 25 Feb '20

25 Feb '20

Dear cgl.ucsf.edu, In chimerax, Helix is disrupted for some reason, could I change the intermediate residues into helix? There are two ways I tried, 1: use 'dssp' command, 2: use 'setattr :467-469/A res ss_type 1'. But both didn't not work. Could you tell me how to change this? Best regards, Meinan [image: image.png]

2 2

Default mrc/ccp4 file opening by ChimeraX
by Kim, Doo Nam 21 Feb '20

21 Feb '20

I use mac (10.14.6). But when I double-click mrc/ccp4 file, chimera automatically opens it. I want to open it with ChimeraX (which is faster). However, even when I right-click on ccp4 file -> open with -> always open with -> ChimeraX_Daily, only that specific file is opened with chimera automatically. Does anyone know how to set up so that all (including future) .mrc and .ccp4 files are opened with ChimeraX? Thank you Best, Doonam

2 2

Error in reopening session
by Maximiliane Wieland 20 Feb '20

20 Feb '20

Hi, When I try reopening a session I have been using for two weeks now (so many saved view :( )and I get the following error: Unable to restore session, resetting. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 653, in restore obj = sm.restore_snapshot(self, data) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot cmd.name_frozen(session, name, Objects(**value)) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/cmd.py", line 54, in name_frozen raise UserError("nothing is selected by specifier") chimerax.core.errors.UserError: nothing is selected by specifier This is the error from the daily build, in the production release one I get the same error, only difference is in "cmd.py", line 52, in name_frozen When trying to open an older version (that I saved but did not open, since I kept using the same session and saved it to the latest version) I am asked to replace missing files, which are in fact not missing but still in the very same directory and with the very same name, so it feels like the real error lies elsewhere? Can I make it reopen the session without reopening the volume? The last version of the session I can open without a problem is close to two weeks old, I named some selections in the meantime, could that cause such an error? I use ChimeraX on MacOS X 10.12.6 I will also submit the bug but since it is kind of urgent I thought I would try submitting here, too, in hopes of a quick response. Best, Maxi

1 0

Set view
by Aritz Roa Eguiara 19 Feb '20

19 Feb '20

Dear ChimeraX, I am trying to produce a script .cxc to open on ChimeraX and I want to set a specific camera position coordinates that can be opened by anyone. I do obtain the position by just using the command camera, but then I do not know how to obtain that position without saving the view. How should this be written on the command line so that anyone can open it and get that view? For example, I know that PyMol allows the get view command to obtain all the information that later only need to be pasted on the script, is there anything similar? Thank you in advance for your help. Best regards, Aritz

2 2

undo/redo move?
by Oliver Clarke 19 Feb '20

19 Feb '20

Hi, I like the expanded undo/redo capabilities in Chimerax - particularly having the capacity to undo selection/deselection and color commands is very helpful. However it seems like there is no undo/redo move functionality. I find myself using this a lot in Chimera, is there any possibility of incorporating this into Undo/Redo in ChimeraX? Basically adding the possibility to Undo/Redo translation, rotation and scaling? Cheers Oli

4 5

workflow suggestions
by Joel Meyerson 17 Feb '20

17 Feb '20

Hi, I'm a reasonably experienced Chimera user making the shift to ChimeraX. So far I'm really enjoying it. I'm writing because the biggest challenge I'm having so far is that there doesn’t seem to be anything quite like the "activate" features in the original Chimera Model Panel. Are the "activate" features available in ChimeraX, or are there plans to implement them? If not, can you suggest a way to achieve a similar degree of agility for manipulating objects in ChimeraX? So far I have been clicking between Right Mouse modes which does not feel so fluid yet. Perhaps there are keyboard shortcuts or other workflow tricks that you could suggest to improve the feel of navigation. Thanks, Joel

2 1

Re: [chimerax-users] [Chimera-users] Default storage folder, ChimeraX
by Elaine Meng 14 Feb '20

14 Feb '20

Hi Martín, Currently there is no way in the user interface to change the ChimeraX downloads location, described here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> You could make a symbolic link to that location, but the files would still really be in the same place. Probably the location can be changed by editing somewhere in the Python code, but somebody else would have to advise on that. You may be interested that there is a separate mailing list for ChimeraX, chimerax-users(a)cgl.ucsf.edu (CC’d on this message). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 13, 2020, at 4:00 PM, Martín González Buitrón <martingonzalezbuitron(a)gmail.com> wrote: > > Dears all, > Hope you are well. > > I have started to use ChimeraX in Ubuntu and I realised that one folder was created with my fetches and other things (i.e. ~/Download/ChimeraX/). > > How can I change this to other of my own preference? > All the best, > Martín

3 2

Reverse color byhet
by Ahmad Khalifa 13 Feb '20

13 Feb '20

If I color byhet then color zone a volume, the volume takes some colors from the hetero atom colors. How to reverse byhet coloring? Regards.

3 3

select menu bundle tags
by Anthony James Schaefer 12 Feb '20

12 Feb '20

Hello Are there any plans to add bundle tags for putting selectors on the select menu? Thanks, Tony

3 2

Color by Conservation in ChimeraX
by Sean Moore 11 Feb '20

11 Feb '20

Hello, I read an older post that color by conservation is pending for ChimerX. Is it available now? When I open a sequence alignment that I generated elsewhere, it shows the alignment and conservation, it identified the correct protein chain, but there is no menu in that window to assign the colors to the protein. (no option to "Again from the Multalign Viewer menu, choose: Structure... Render by Conservation. This will call Render by Attribute, in which…”) Should I use Chimera for this instead of ChimeraX? Sean

3 4

Reproduce exact view
by Christophe Leterrier 11 Feb '20

11 Feb '20

Hi, I haven't been able to find how to - log - set - store - recall a precise view (ie get the same exact image if I do a snapshot). First use case would within the same session (fixed computer, window size, no restart of the application in between). Second use case (more tricky?) would be independently of computer / window size / current session. Thanks for your help! Christophe

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Re: [chimerax-users] Crossfade rough transition while making a movie
by Elaine Meng 07 Feb '20

07 Feb '20

Hi Ahmad, This appearance of snapping to the position may not be very avoidable, because “view” transitions just take a linear path and it always looks somewhat abrupt (to me anyway) when it reaches the endpoint. There is currently no option to make it go slower when it is closer to the end. You could try saving an additional position along the way and using it as an intermediate and then going slower after the intermediate by using more frames per distance, and/or you could try adding a few extra wait frames between when it reaches the endpoint and when it starts the crossfade, for example: view pos6 50; wait 100 crossfade 50; view pos5; wait 50 (OR: crossfade 50 viewpos5 50; wait 50) However, I don’t know if either of those would help much. When I’m making a movie I usually end up experimenting a lot with numbers of frames in movements and waits, but the sharp endpoints of view transitions are not currently avoidable as I understand it. Best, Elaine > On Feb 7, 2020, at 1:10 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Hi Elaine, > > Sorry if my description was vague. With the modification you suggested, I still have the rough transition between pos6 and pos5 but with a slower crossfade into pos5. > > I attached my movie (made with script in the original post) to get a better idea of what I mean. At 0:2, pos6 appears like it snaps in place, then the crossfade into pos5 occurs. > > Is there a way to make the transition smoother? > > Regards. > > On Fri, Feb 7, 2020 at 12:18 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ahmad, > Not sure I understand what you actually want, but I’ll try to answer anyway… > > If you mean you want to see a gradual change in position from pos6 to pos5 then you would need to put a frames number after pos5, for example: > > crossfade 50; view pos5 50; wait 50 > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > (Crossfade does not interpolate the movement, you have to do it with the view command.) > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> > > Some minor notes on scripts. You do not need “;” at the end of any line; it is only needed to separate commands that are on the same line as each other, as in the example above. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 6, 2020, at 11:59 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > I want to crossfade pos6 into pos5, the crossfading itself is smooth, but the below script gives me an abrupt transition at the start of the crossfade (at pos6), how can I fix that?! > > > > view pos4 > > wait 30; > > > > movie record supersample 3 size 1920,1080 > > view pos6 50 > > wait 50; > > crossfade 50; view pos5 > > wait 50; > > movie encode IJ_movie3.mp4 quality high > > <IJ_movie3.mp4>

2 1

Crossfade rough transition while making a movie
by Ahmad Khalifa 07 Feb '20

07 Feb '20

I want to crossfade pos6 into pos5, the crossfading itself is smooth, but the below script gives me an abrupt transition at the start of the crossfade (at pos6), how can I fix that?! view pos4 wait 30; movie record supersample 3 size 1920,1080 view pos6 50 wait 50; crossfade 50; view pos5 wait 50; movie encode IJ_movie3.mp4 quality high

2 1

Command line interface is detached
by Ahmad Khalifa 04 Feb '20

04 Feb '20

My command line interface used to be attached at the bottom. Now it's floating on the screen and the only way I could attach it back is to place it in the right panel. How can I attach it back to the bottom of the screen, spanning the entire length of the ChimeraX window? P.s. I'm running Linux Centos 7.

2 1

Chimerax on a HPC cluster
by Thu Nguyen 01 Feb '20

01 Feb '20

Dear all, I administer a small HPC cluster (Rocks 7) at a bio research institute and a user has requested Chimerax to be installed on it. Has anyone successfully done so ? If yes, I wish to help some hints as to how it is done and an assessment of how it performs . Thanks and regards Thu D. Nguyen Systems & Computational Biology Platform Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne www.bio21.org

2 1

question about ChimeraX Hide Dust Feature
by Philip Schmiege 30 Jan '20

30 Jan '20

Hi I just downloaded the new ChimeraX, and was wondering where the Hide Dust option is located. I cannot find it. Any help is greatly appreciated! Philip _____________________________________ Philip Schmiege Graduate Student in Biophysics Li Lab, Dept. of Molecular Genetics, L5.162 philip.schmiege(a)utsouthwestern.edu ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 3

Fwd: Colors from snapshots
by Christophe Leterrier 29 Jan '20

29 Jan '20

Hi, I wonder why the colors in the snapshots (and movies) from ChimeraX are always washed-out compared to the colors I get live in the viewer. Attached is a screenshot with the viewer on the left, the corresponding snapshot on the right: one can see how the snapshot is desaturated compared to the viewer. From my limited tests it is the case when saving as both PNG and PPM, and I wonder if this could be corrected. I could saturate the screenshots afterward but it doesn't seem right to me to grossly mess with color levels post-hoc given how stunning the shaded rendering from ChimeraX are. Thanks, Christophe

3 5

Scripting Resources
by llehmann＠uoregon.edu 28 Jan '20

28 Jan '20

Hello, I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time. Best, Lauren Lehmann Biochemistry Graduate Student University of Oregon

3 4

volume morph
by Karim Rafie 28 Jan '20

28 Jan '20

Dear all, I would like to create a morph movie between two volumes in ChimeraX, however I am having difficulties with generating it. I am using the following command (e.g.) to "create" the morph: volume morph #1,2 frames 50 After it has completed I get a new volume but I can't review the frames themselves, i.e. the output is a new map. I tried scouring the tutorials and command page but can't find a solution. I tried it with the ChimeraX Ubuntu 16.04 distribution as well as the generic linux version. Any help would be greatly appreciated. Best wishes, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden

3 4

interface residue plot save as text file?
by Marta Perez Illana 28 Jan '20

28 Jan '20

Hi alI I have very recently started to play around with ChimeraX. I am trying to use the interface functionality as a substitute of traditional find contacts/clashes ( I am aware of the differences but I think for my purpose are both fine). I would like to save somehow the "interface residue plot", rather than the image of the plot per se, a kind of text file for example... is there a straight fordward way that am I missing? Thanks!! Marta

2 1

SMILES structures
by Eric Pettersen 28 Jan '20

28 Jan '20

Hi all, SMILES strings can now be translated to 3D structures (via NIH NCI or Indiana University web services), e.g. “open smiles:c1ccccc1”. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 1

dome camera mode
by James Hedberg 24 Jan '20

24 Jan '20

Hi, I see from previous threads (3/2019) that there are no plans to add the dome projection/fisheye mode for the camera control on ChimeraX: "It would take some days of work to add dome camera mode to ChimeraX. We have no funding for that and very few people will use it so I'm afraid that is not likely to be implemented.” I understand there is probably not a lot of current demand for this feature, however, in the spirit of Field of Dreams - if you build it, they will come. There is a growing interest in using planetariums/full domes for non-astro related sci-viz, yet very few tools available to do so. We’re currently using Chimera (regular) to do sci-viz in the planetarium for proteins and more. Knowing that this would be supported down the road when ChimeraX takes over (not sure when that will happen) would certainly be nice. You could make ChimeraX uniquely positioned to fill this deficit. Anyway, just a hand raised here for an informal poll of ‘who wants dome mode’. Thanks, James Dr. James Hedberg Physics Lecturer Director, CCNY Planetarium<https://ccnyplanetarium.org> City College of New York Department of Physics

2 6

ChimeraX and REST service interoperation
by Mungo Carstairs (Staff) 24 Jan '20

24 Jan '20

Hi, With your helpful hints, I have a version of Jalview interacting with ChimeraX in the same way it can already with Chimera, over the REST interface. Functionality includes loading structures, aligning, colouring, raising labels on structure on mouseover in Jalview, and exchange of residue features/attributes. I have just one interaction not working yet: highlighting residues in Jalview when a selection is made in ChimeraX. - Jalview starts listening for ChimeraX selections with (e.g.) info notify start selection jalview prefix SelectionChanged url http://localhost:49981/jalview/chimera1 - user makes a selection in ChimeraX - ChimeraX sends GET?chimerax_notification=SelectionChangedselection+changed - Jalview send 'info selection level residue' - no response / timeout; ChimeraX log reports 'broken pipe error' Exception happened during processing of request from ('127.0.0.1', 50714) Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 316, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 347, in process_request self.finish_request(request, client_address) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 360, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 720, in __init__ self.handle() File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 426, in handle self.handle_one_request() File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 414, in handle_one_request method() File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 97, in do_GET self._run(args) File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 174, in _run self.wfile.write(data) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 799, in write self._sock.sendall(b) BrokenPipeError: [Errno 32] Broken pipe NB this is all before a response has been sent to the 'SelectionChanged' message. Any idea what the problem is here please? Do I need to reply to the first message before sending another? The same mechanism does work ok with Chimera. Thanks, Mungo p.s. I noticed the 'listinfo' command (undocumented) seems to behave like 'info'. Should I continue to use 'list' or switch to 'info'? * [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

2 3

PubChem
by Eric Pettersen 22 Jan '20

22 Jan '20

Hi all, As of tomorrow’s build, ChimeraX will be able to fetch PubChem entries, e.g. “open pubchem:2519” or “open 2519 from pubchem”. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Next/previous buttons for model display/activation?
by Oliver Clarke 21 Jan '20

21 Jan '20

Hi, I use the Next/Previous buttons in the lower portion of the Chimera GUI all the time for quickly cycling through maps/models (e.g. when inspecting the results of 3D classification). Would it be possible to bring these to the model panel on ChimeraX? Cheers Oli

2 1

Re: [chimerax-users] silhouettes on mesh in ChimeraX
by Tom Goddard 21 Jan '20

21 Jan '20

Hi Gabe, I agree the silhouette edges look bad on meshes. ChimeraX cannot turn off silhouette edges on just meshes. It uses the scene depth at each pixel to compute the edges and the mesh contributes to the scene depth. This is a different method than Chimera used. It has the advantage that it renders basically as fast as without silhouettes where Chimera renders about 2x slower with silhouettes. The Chimera method won't work in ChimeraX because ChimeraX uses modern OpenGL (core profile) which no longer supports drawing linewidth greater than 1. The Chimera algorithm worked by drawing the edges of every triangle in the scene with linewidth 2 and slightly behind the triangle. This linewidth 1 only limitation of modern OpenGL also is a problem with meshes on retina displays where the lines are too thin and hard to see. At any rate, there are ways to provide silhouette edges only on some models but not meshes. But they are hard to implement. I'll make a ticket for it but don't expect to be able to do it with our limited resources. https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2765 So the best advice I have is show the atomic model and mesh without silhouettes or use Chimera. Tom Examle of mesh with silhouette edges > On Jan 18, 2020, at 4:01 PM, Gabriel Lander <glander(a)scripps.edu> wrote: > > Hi Tom, > One of the "go-to" representations to demonstrate the quality of a modeled PDB in an EM density is sticks shown in a volume mesh. In Chimera when you turn on silhouettes they would only show around the atoms, but not the mesh. This is not the case in ChimeraX, and renderings with silhouettes and meshes look really messy. Is there a way to specifically turn off silhouettes on meshes but not atoms? > Thanks, > -gabe > >

1 0

How to batch process structures?
by jacky zhao 21 Jan '20

21 Jan '20

Hi everyone, I have tried to use chimeraX yesterday. It is vey cool! I just wonder how to batch process the structures? We will generate more than thousands of structures and will analysis the binding interface. Can I use chimeraX to instantly show the interface interactions one by one? Thank you for your time. Jacky

3 5

Exporting image in 300 DPI
by Hassan Ahmed 21 Jan '20

21 Jan '20

Hello, I wanted to ask if it is possible on ChimeraX to export image with 300 or 150 DPI? I can not find a possible selection tool as the older chimera versions. Is there a certain command or an option to do it? Thank you in advance, Regards, Ahmed -- Ahmed Hassan Institute of Plant Biology Braunschweig University of Technology Spielmannstrasse 7 38106 Braunschweig Germany Tel: +49 - 531 - 391 5885 e-mail: a-a.hassan(a)tu-braunschweig.de

2 1

Tile a vseries
by Sean Connell 17 Jan '20

17 Jan '20

Hello, I was wondering if it is possible to tile multiple volume series such that one can have 2-3 series playing side by side? If so could you suggest the syntax for the tile command I cannot seem to get it right? I have the two vseries loaded as #1 and #2 (and each series has 10 sub volumes). I have tried variations of tile #1,2 columns 2 spacingFactor 1 and get errors like this: Traceback (most recent call last): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 258, in execute cmd.run(cmd_text) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2837, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in tile spacing = max([m.bounds().radius() for m in models]) * spacing_factor File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in <listcomp> spacing = max([m.bounds().radius() for m in models]) * spacing_factor AttributeError: 'NoneType' object has no attribute 'radius' AttributeError: 'NoneType' object has no attribute 'radius' File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in spacing = max([m.bounds().radius() for m in models]) * spacing_factor Thanks in advance for any suggestions you have. sean

2 1

Save scene like in "Chimera"
by Lau Kelvin 17 Jan '20

17 Jan '20

Hello all, Is there a save scene command like in chimera. I have found the command for positions via “view”. If not, its back to saving many sessions at the moment. Best, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin.lau(a)epfl.ch<mailto:kelvin.lau@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267>

3 4

Show active site metal and ligand in morph
by Yifan Wang 16 Jan '20

16 Jan '20

Dear chimeraX developer, I am a graduate student from university of Texas at San Antonio. I’m trying to make a movie to compare two of my structures (resting state and substrate bound) using the function “morph”. But there is a problem, I very appreciate if you can help me figure this out. As show in Figure 1, I have two structures superposed. The resting state (nude) contains an active site metal ion coordinated by three residues and 3 water molecules. And the substrate bound (blue) also contains a metal coordinated by the same residues, a remaining water molecule, and a new ligand as my substrate. After I entered command “morph #1,2 frames 60”, I got the result of Figure 2. However, the active site metal ion and the water and substrate are missing. I want to show the active site changes between model 1 and 2. Model #3.1 seems keep the metal coordination bonds but I can’t make it present even with “show”. So my question is how to show the metal and the corresponding ligands in morph? Regards, Yifan Wang [cid:143A130E-412D-4674-AB95-99EA0C21DF44@UTSARR.NET] [cid:90E28A3D-AB8F-402F-A982-8B40682176A1@UTSARR.NET]

2 6

Re: [chimerax-users] [Chimera-users] Chimera X commands
by Elaine Meng 14 Jan '20

14 Jan '20

Hi Drew, You may be interested that there is also a mailing list specifically for ChimeraX questions: <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> We’re glad you like Chimera! For ChimeraX we wanted to make various command-line improvements such as to make it easier to specify chains, to give several commands more obvious names or make them easier to use, etc. If you download ChimeraX the User Guide is in the Help menu, with the top page being an index of tools and commands that links to their individual pages. We also have a copy of the User Guide at our website: <http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html> The User Guide includes a page on the ChimeraX atomspec syntax and another on how it is different from Chimera’s. <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec-diffsum.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 13, 2020, at 9:53 PM, Andrew Waight <waight(a)msg.ucsf.edu> wrote: > > Hello all, > I've been an exclusive Chimera user for over 15 years. I have been scripting a lot in python lately and am super excited to learn that ChimeraX is written in python3. I totally want to import some chimera functions into my programs. Problem is, the ChimeraX command syntax seems all new (i can't even really figure out how to select properly, is there a ChimeraX command index that I am missing and is ChimeraX for me? ChimeraX looks beautiful by the way. Thanks you guys are amazing! > Drew

1 0

Show dashed lines after hiding atoms
by Ahmad Khalifa 10 Jan '20

10 Jan '20

How can I show the dashed lines that signifies an interruption in the structure after I do "Hide model-spec atoms"? Regards.

2 1

Chains with symbol ID such as % and $ cause errors
by Ahmad Khalifa 08 Jan '20

08 Jan '20

I can do "show #2/m cartoons" for a chain with ID m, but for a chain with ID % or $, I get: show #2/% cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword

2 2

Copy/combine function in ChimeraX
by Ahmad Khalifa 07 Jan '20

07 Jan '20

How do I duplicate (back up) a model that I already have open in ChimeraX? Regards.

2 1

ksdssp equivalent in Chimerax
by Elliott, Jabari 07 Jan '20

07 Jan '20

Dear users, I was wondering if there was a way to adjust the preset thresholds for betasheet and helix depictions in chimerax. Essentially, I am looking for a “ksdssp” command equivalent. - “Ksdssp –s 2” Best, Jabari

2 1

differentiating file category
by Anthony James Schaefer 02 Jan '20

02 Jan '20

Hello, Is there any way I can get a bundle to know that I'm trying to open a file from a certain category (e.g. Molecular structure vs. Molecular trajectory) from the File -> Open... menu? I'm trying to build a plugin that will allow me to open Gaussian log files in ChimeraX. I'd like to have it open the optimized structure when I go File -> Open... and change the file filter to "Molecular structure files". When I set the file filter to "Molecular trajectory files", I'd like it to open the log file as a trajectory with each frame being one of Gaussian's optimization steps. The file stays the same, I just want to have my 'open_file' method know that it should open the file differently. So far, I've tried having multiple 'Open' entries in my bundle tags. Here are some relevant tags from my setup.py: "ChimeraX :: DataFormat :: LOG :: Gaussian output file :: Molecular structure :: .log :: :: :: :: :: Gaussian output file :: utf-8", "ChimeraX :: DataFormat :: LOG trajectory :: Gaussian output trajectory :: Molecular trajectory :: .log :: :: :: :: :: Gaussian output file :: utf-8", "ChimeraX :: Open :: LOG :: Gaussian output file ::", "ChimeraX :: Open :: LOG trajectory :: Gaussian output trajectory :: :: coordsets:Bool", My 'open_file' definition line is: def open_file(session, path, format_name, coordsets=False): While I'm testing, I've set up my 'open_file' method to print the arguments that get passed to it. When I use File -> Open..., I can see that 'format_name' is always "Gaussian ouput file" (never "Gaussian output trajectory") and 'coordsets' is always False, regardless of the file filter. When I use the `open` command (`open asdf.log coordsets true`), 'coordsets' is True and 'format_name' is "Gaussian output file". I can work with the open command because of the 'coordsets' argument, but I'd like to know if there's something I can do with the File -> Open... menu. Thanks, Tony

3 2

Superimposition of Carbohydrate Molecules
by Rajarshi Roy 19 Dec '19

19 Dec '19

Dear ChimeraX, I am trying to superimpose multiple carbohydrate chains using chimeraX. Using match command, I am unable to do the same. Here is my command: *match #2:1-4 to #1:1-4* But I am getting the following error: Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'match' command to superimpose small molecules/ligands. Already I am using match command, still why the same error is showing? Please advise me on how to proceed? Thank you in advance. -- *with regards* *Rajarshi Roy* *PhD Research Scholar* *Biosciences and Biomedical Engineering* *Indian Institute of Technology, Indore* *India*

2 2

Amber trajectories
by Lewandowski, Jozef 16 Dec '19

16 Dec '19

Hi, Quick question. Are there any plans for ChimeraX to support opening also Amber trajectories (as Chimera does)? Thanks, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

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Re: [chimerax-users] [Chimera-users] view MD ChimeraX
by Elaine Meng 16 Dec '19

16 Dec '19

Hi Fabian! The “Molecular Dynamics Viewer" tool is available on ChimeraX Toolshed from outside developers, i.e. it is not written by our group. However, the description on Toolshed pretty much says what it does: it is a simple graphical interface for showing multiframe PDB files as a trajectory. It doesn’t read other trajectory formats. <https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer> After you install it, it will be under Tools… General in the menu. Starting the tool from that menu will open a window in ChimeraX and then clicking the Open button in that tool will allow you to browse to and open a multiframe PDB file, like 1PLX.pdb downloaded from the RCSB PDB (NMR structure, so it has multiple conformations each as a MODEL in the single PDB file). Then you can use the other buttons, e.g. Start to play as a a trajectory. (I wasn’t sure what you meant by “not able to use it.”) However, *without* this tool: Just using ChimeraX without installing anything extra, you can read in a few trajectory formats and then play them with the “coordset” command or using a slider interface shown with “coordset slider". The trajectory formats known to ChimeraX are listed here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory> <http://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> See also “coordset” and “coordset slider” <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. There is also a chimerax-users(a)cgl.ucsf.edu mailing list, CC’d here. > On Dec 15, 2019, at 1:50 AM, Fabian Glaser <fglaser(a)technion.ac.il> wrote: > > Hi, > I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. > Can you please help me? > Best, > Fabian

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SSL expiry
by James Walshe 13 Dec '19

13 Dec '19

Hi Guys, Hope you’re well. I’m trying to download some ChimeraX plugins. It appears the toolshed security certificate has expired. https://cxtoolshed.rbvi.ucsf.edu/ Just letting you know if you were unaware. Kind regards, James ______________________________________________________________________ The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System.

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multiple conformations in one pdb chain
by Linda Schulte 12 Dec '19

12 Dec '19

Hi everyone, I have two conformation in a single PDB chain, see example below: ATOM 90444 N APHE z 9 253.604 183.844 259.994 0.50 47.28 N ATOM 90455 N BPHE z 9 253.778 183.499 258.715 0.50 47.28 N Chimera can read in this two conformations of the chain, while chimerax shows only the A atoms of the chain. How can I read in also the B atoms? Thanks a lot for your help. Best, Linda -- Linda Schulte Goethe-Universität Frankfurt am Main Institut für Organische Chemie und Chemische Biologie, AK Schwalbe Max-von-Laue-Straße 7 D-60438 Frankfurt am Main N160/300 +49 (0)69 / 798-29956 schulte(a)nmr.uni-frankfurt.de

2 1

Saving ChimeraX session error on macOS
by Yixiao Zhang 11 Dec '19

11 Dec '19

Dear all, I'm preparing a movie in chimeraX on macOS. There are more than 25 maps opened and also another 20 low-pass filtered maps generated within chimeraX by "vol gaussian". There are also ~20 pdb models, several positions saved by "view name" and ~20 2dlabels. I got the following error message when I save the .cxs file, and the session was not saved. RuntimeError: Unable to restore objects of LabelModel class in ChimeraX-Label bundle because the class name is not listed in the name to class table for session restore File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) See log for complete Python traceback. The session is still alive, and I have no problem when I save other much simpler sessions. Is there a way that I can get this big session saved? Is the error related to 2dlabels? Many thanks, Yixiao

2 6

Starting ChimeraX programmatically with remotecontrol
by Mungo Carstairs (Staff) 11 Dec '19

11 Dec '19

Hi there, Jalview has the ability to launch Chimera with "--start RESTServer", capture the port number from the response, and drive Chimera with REST commands. I'm trying to figure out whether this mechanism is also provided with ChimeraX. I've read http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-July/000113.html and looked at http://www.rbvi.ucsf.edu/chimerax/docs/user/startup.html and http://www.rbvi.ucsf.edu/chimerax/docs/user/options.html#start but so far I can't see that "RESTServer" is a startable tool. Is this, or is it planned to be, possible somehow? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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Rotate bond move large/small option in VR
by Lewandowski, Jozef 09 Dec '19

09 Dec '19

Hi, Is there a way to change the option from the default “move small” to “move large” of the Bond rotation tool in VR? Ideally, it would be great if I could switch between these options on the fly with some combination of buttons on the controllers. If nothing like that is implemented is there a way I could change the “move” default for the Bond rotation tool in VR using the command line? Thanks, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

3 7

Relative paths to source files in saved sessions
by Christophe Leterrier 04 Dec '19

04 Dec '19

Hi, I'm working on multiple Chimera sessions on different computers, syncing the content of the folders and cxs files. However when opening a cxs file on a different computer, I have to manually relocate all the source files every time (in my case tif stacks, and even navigate for each of them from the cxs folder to the source files folder because the folder is reset at every source file selection). Would it be possible to somehow store the relative path between the cxs file and the source files in the cxs file, or try relative if absolute paths fail? I have no idea how this is done currently, so sorry if this is an unrealistic/undesirable proposal. Thank you, Christophe

2 1

Main interface does not start
by Thomas G. Laughlin III 04 Dec '19

04 Dec '19

Hi, I've been using ChimeraX 0.9 for a while, but today when I tried to open it, the group photo comes up and "initializing bundles" then disappears without starting the main interface/GUI. I recently installed items from the toolshed for the first time (2 days ago but ChimeraX worked the day of install) and I tried re-installing ChimeraX without success. This is on a Windows 10 OS with intel integrated graphics. Any suggestions on what to do to diagnose and correct the problem? Thanks for the help, -Tom -- Thomas G. Laughlin III PhD MCB (BBSB, Candidate) | *Univ. of California-Berkeley* | Present BS Biochemistry | *Univ. of Missouri-Columbia* | 2014 t.laughlin(a)berkeley.edu <thomas.laughliniii(a)gmail.com>

2 1

Fw: Multi-user sessions: development
by Williams, Joanne 03 Dec '19

03 Dec '19

________________________________ From: Grime, John M. <jgrime(a)ou.edu> Sent: Monday, December 2, 2019 1:12 PM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Multi-user sessions: development Hello! We have some use cases where multi-user VR sessions in ChimeraX would be very useful. We already have out own in-house networked VR software, and I was wondering if the source code to ChimeraX is available for academic users so we can see if we can add similar functionality? Thanks! John Grime, Ph.D. Emerging Technologies Developer University of Oklahoma Libraries

3 2

Segment map feature only available to Mac users ?
by WERNERT Florian 29 Nov '19

29 Nov '19

Hi ChimeraX users developers and maintainers, I've been able to experiment with the segment map<https://www.cgl.ucsf.edu/chimerax/docs/user/tools/segment.html> feature provided by Segger package on the Mac daily-build, on a colleague's Mac. However I downloaded the Linux daily build on my Linux machine and it appears that this function is not present in the menu. Is it a bug or is the "segment map" feature only available to Mac ? If this is the case, would someone be able to give some guidance on how to port the feature to Linux ? I'm quite experienced in C, C++, Java and Python coding, having the coding skills shouldn't be an issue in order to do it. Thanks, Florian W

2 2

ChimeraX stalls when trying to display surfaces from a (strange) group of atoms
by Christophe Leterrier 27 Nov '19

27 Nov '19

Hi, I'm trying to use ChimeraX to visualize Single-Molecule Localization Microscopy (SMLM) data. In short, the output of an SMLM acquisition and processing is a list of fluorophores XYZ coordinates with associated uncertainty, that can be used to reconstruct a 3D image. I have made a script that make a pdb file from these localization so that I can directly display the resulting structure as if it was a protein with a number of random atoms (the only difference is that angstroms in ChimeraX are really nanometers in my data). The rendered pqr file is here (I use a pqr pdb format to specify the radius to the localization uncertainty, hence the variable diameter of each sphere): http://www.neurocytolab.org/up/Example_File.pqr The rendering with the "Spheres" view of atoms works well, see a screenshot here: http://www.neurocytolab.org/up/Render.png However, when I try to get the enveloppe of the resulting object using the "Surfaces" display (click on Surfaces>Show), ChimeraX hangs (I'm on OSX and get the dreaded infinite rainbow beachball). Is there a chance that I can get ChimeraX to render the enveloppe object this way, or is it really too far from what it's supposed to do? I can imagine that I'm trying to use ChimeraX for something completely different than its intended use, but it definitely has a lot of potential for this. Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

4 4

Color key
by Ricardo Righetto 18 Nov '19

18 Nov '19

Hi, Apologies if this has already been asked or documented somewhere, but I could not find it. Is there a way in ChimeraX to create a bar showing the color scale ("Color Key" in Chimera) e.g. when coloring a map by local resolution? Thank you! -- Ricardo Diogo Righetto

2 1

How to select one of ligands which is named in different numbers
by Meinan Lyu 11 Nov '19

11 Nov '19

Hi, I am having trouble in how to select one of the ligands which named LIG 1, LIG 2, LIG 3, LIG 4, etc. when I hide all of them and want to specifically show LIG 1, using "show LIG 1 target a" command does not work. How to deal with this that the ligand name have a space inside? Thank you very much. Best regards Meinan

2 1

surface cap transparent when surface dust on ?
by bertrand beckert 06 Nov '19

06 Nov '19

Hi All, I have been recently trying to color a volume by a map value... So far it worked really well using the color command.... color sample #1 map #2 offset 0.1 palette " values" But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera? Also another thing, I usually do is the following: open volume1.mrc volume surfaceSmoothing true surface dust #1 lighting soft Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes... Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent? Thanks for the hard work and the nice software! Best Bertrand

3 3

Catalina woes
by ubaumann 05 Nov '19

05 Nov '19

Dear all I am trying to use ChimeraX after a clean install upgrade to Catalina, OSX 10.15.1 I get the attached error message that the software can’t be scanned for malicious code Is there any way around this, please? Same holds for Chimera ( and other programs….) Thanks a lot! Kind regards, Ulrich

2 1

Trouble initializing ChimeraX on CentOS
by Brown, Alex 18 Oct '19

18 Oct '19

Hello and good morning, I have always had a great experience using Chimera and so I was hoping to try out ChimeraX for some of our larger cryo-em data sets. However, following download and an install that did not seem to produce an error message, I can not seem to initialize the program. I have copied the output from the command prompt below. Beyond that, I should probably also mention that we are running the centos-release-7-6.1810.2.el7.centos.x86_64 operating system with intel chips and nvidia graphics cards. [root@gaolab ~]# chimerax-daily NOTE: available bundle cache has not been initialized yet WARNING: could not retrieve bundle list from toolshed NOTE: Traceback (most recent call last): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 871, in <module> exit_code = init(sys.argv) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 580, in init check_available=opts.get_available_bundles) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 1681, in init _toolshed = Toolshed(*args, **kw) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 359, in __init__ if not available.has_cache_file(self._cache_dir): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/available.py", line 109, in has_cache_file return os.path.exists(os.path.join(cache_dir, _CACHE_FILE)) File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType BUG: TypeError: expected str, bytes or os.PathLike object, not NoneType File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) _See log for complete Python traceback._ Thanks in advance for any support you may be able to provide on this! -Alex Alexander Brown IV, PhD Postdoctoral Researcher Horae Gene Therapy Center Li Weibo Institute for Rare Diseases Research University of Massachusetts Medical School 368 Plantation Street, AS6-2011 Worcester, MA 01605 Phone: (508) 856-3316 Email: alex.brown(a)umassmed.edu<mailto:alex.brown@umassmed.edu> Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

2 1

problem of chimerax
by 陈柳青 18 Oct '19

18 Oct '19

Hello! I tried install either daily builds or release 0.9 of chimeraX on my win10 64 system, but both encounter the same problem showed in the attachment. After startup, i can't see any menu! but when i move mouse on the menu , it will appear sub menu. How can solve this bug? sincerely Liuqing chen

2 1

macOS Catalina gives PermissionError opening files
by Tom Goddard 16 Oct '19

16 Oct '19

If you are thinking of upgrading to the new macOS Catalina (10.15) and want to use ChimeraX on it you might hold off. We have found that opening files using the ChimeraX open command or the recent files thumbnails often causes PermissionError and fails to open the files. This is caused by a new macOS Catalina security feature when any app that tries to open a file under Desktop, Downloads, or Documents must first raise a permission dialog asking if the app is allowed to open files from that directory. When using the ChimeraX File / Open dialog (from the File menu) the permission dialog is shown and works. But if you use the ChimeraX open command of recent files thumbnails on directories that you have not granted permission for with the Open dialog, then those fail with PermissionError -- apparently those methods of opening are not able to show the permission dialog. Other applications (e.g. photo editing program Gimp) have the same problem. We do not yet know how to solve this. Tom

2 2

Re: [chimerax-users] [Chimera-users] surface color
by Elaine Meng 14 Oct '19

14 Oct '19

Hi Mike, So close! You’re only missing the “palette” keyword before “rainbow” … try: color height #1 center 0,0,0 axis z palette rainbow <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> (By the way, there is a chimerax-users(a)cgl.ucsf.edu list CC’d here if you have questions specifically about ChimeraX.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 14, 2019, at 2:43 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > I’m trying to do the same thing as Chimera’s “Surface Color”, but in ChimeraX, on the command line. After reading the docs, I tried “color height #1 (the map designation) center 0,0,0 axis z rainbow”. It gave “expected a keyword”. What did I miss? > Thanks, > Mike

1 0

show stands' arrows a little werid
by Meinan Lyu 14 Oct '19

14 Oct '19

Dear Dr., The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much！ Best regards, Meinan CWRU

3 5

Soft lighting changes when additional model is displayed
by Gabor PAPAI 14 Oct '19

14 Oct '19

Dear ChimeraX team, If I open a second model in ChimeraX (0.91) the ambient occlusion in soft lighting mode on the first model disappears or becomes diminished. How can I revert this effect? I attach an image to illustrate this phenomenon. The only change between the two displays that I opened a model of DNA and placed close to the first model. Best regards, Gabor [cid:6AAD58A0-1B6C-4362-8C29-57D033327EBF@igbmc.u-strasbg.fr] --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 4

issues with rotamers tool
by Llorente, Alejandro 09 Oct '19

09 Oct '19

Hi, I am new PhD student using ChimeraX and I am very interested in learning how to work with this program. I am trying to introduce some mutations in my protein in some specific amino acids that I have selected. When I introduce an Alanine in my position of interest (using dunbrack) I have no issues, but when I try any other amino acids (as Phe or Thy) the program has no problem giving me the prediction for the rotamers, but I have some issues. After select some of the most probable rotamers, all the amino acids of my protein change to that kind of amino acid (not just the specific one that I have selected). Another problem is that I have is that when I select a specific atom of an amino acid, the program also select similar atoms but in all the others amino acids of my protein. I really hope that someone can help me with these issues. Thank You very much Alejandro Llorente. Lab of Dr. Nancy Carrasco. Department of Molecular Physiology & Biophysics, Vanderbilt University. 2215 Garland Ave Nashville, TN 37232-0615, room 711. Mobile phone: +34 626586236

2 1

Unable to use Viewdockx
by Abhijeet Kumar 07 Oct '19

07 Oct '19

hi, I am a college student and I am working on a project on protein docking visualization and came across ChimeraX. I am not able to use Viewdockx and the user guide for viewdockx gives a 404 page not found error. So, can you help me with this? Thank you.

2 2

Cuved helix tubes
by Ernesto Arias Palomo 02 Oct '19

02 Oct '19

Good morning, We are using the modeHelix tube to represent the secondary structure. However, our structure contains some long and curved helices, and the representation does not follow their shape with enough precision. Is there any option to increase the fit of the tube to the overall shape of long helices? Thank you very much for your help. Kind regards, Ernesto. -- Ernesto Arias Palomo, PhD Group Leader Biological Research Center (CIB-CSIC) Ramiro de Maeztu, 9. 28040. Madrid. Spain earias(a)cib.csic.es +34 91 837 31 12 ext 4446

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Calculation of polar and apolar surface area
by Gorman, Scott Daniel 02 Oct '19

02 Oct '19

Hi All, I was wondering if anyone has a preferred way of calculating the polar and apolar surface areas for a macromolecule with ChimeraX? I've tried deleting all of the solvent and then using the command "measure sasa @N @O @S" for the polar surface area and then "measure sasa @C" for the apolar surface area, but the calculation for either comes up with a number too close to the total surface area, i.e. apolarSASA + polarSASA > totalSASA. So clearly I'm not approaching this problem correctly. Scott Gorman PhD Candidate Boehr Lab PSU Chemistry

2 1

GUI not properly visualized
by Pascal Albanese UU 25 Sep '19

25 Sep '19

Hi Chimera staff, i just changed PC ad now i have huge visualization problems of the GUI, when opening is fine but when i open any pdb file or session all buttons and commands in the window disappear. Command line actually works but all i see is this: [image: image.png] do you have any explanation? i tried different releases (0.9 official, daily builds) I'm using W10 enterprise, 64bit, intel i9 9900, UHD graphics 630. Thanks for the support, best regards, -- Pascal Albanese Ph.D PostDoc Biomolecular Mass Spectrometry and Proteomics Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan 8 3584 CH, Utrecht The Netherlands Telephone: +31 30 253 6805 https://www.hecklab.com/

2 4

ray tracing
by Ahel,Juraj 24 Sep '19

24 Sep '19

Dear all, pardon me if this has already been answered elsewhere, but I failed to find any information about this in the publication, webpage, or the mailing list archive. Is there a way to generate images of ray-traced maps in ChimeraX? I was often using it in Chimera but I can't find the option to do it in ChimeraX. Was it not included as a feature? Many thanks! Juraj

2 1

Manually imposed symmetry
by Shahid Khan 16 Sep '19

16 Sep '19

Hello I am having difficulty in manually imposing symmetry on a map (*.mrc file) and then extracting the unit cell for the subsequent fitting of PDB structures with fitmap. (1) When I use the command "Volume symmetry #1, C33 axis z centerIndex 107.5" I get the error message "No placements for #1" that I do not understand. (2) I cannot figure out from the help documentation on how to save and display one of the created segments. Any ideas? Thanks Shahid -- Dr Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory

3 4

render buriedArea surface?
by Alexis Rohou 10 Sep '19

10 Sep '19

Hi all, I would like to depict the buried surface area between two chains. I have used "measure buriedarea" to measure it, and I can use "surface" to display the surfaces of either set of atoms, but I'd like to depict the surface of one of the chains, highlighting the region buried by the other chain. Is there a way to do this in ChimeraX? If not, does anyone have a recommendation as to how to achieve this? Perhaps by pre-computing the surfaces in another program? Thanks in advance! Cheers, Alexis

3 6

vdw representation in chimeraX
by Elena Zehr 09 Sep '19

09 Sep '19

Hello, In chimera one can display dot van der Waals surfaces for atoms. *vdw* *atom-spec* <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> What would be the equivalent command in ChimeraX? Thank you, Elena

2 2

Open days EPFL - ChimeraX VR
by Krapp Lucien Fabrice 05 Sep '19

05 Sep '19

Hello, We are creating some small VR demos in ChimeraX for the EPFL open days in a few weeks (https://www.epfl.ch/campus/events/celebration-en/portes-ouvertes/) It is an event to show to a broader audience what the university is doing. The demos consists of small proteins up to density maps of bacteriophage with a few simple animations and menus to interact with the structures. Everything is almost done, I'm currently trying to fix the last issue but I didn't find a solution in the documentation. For two of the demos we would like the user to move a selection in VR with one of the VR controller right out of the box without having to go in the VR menu and click on the "move selected" button. I was able to make it work on Linux by loading the session though the remote API with the right part selected but it doesn't seem to work on Windows. The log shows a status change when clicking on the button "move selected" in VR but not the actual command to change the mode. Do you know if there is a way to change the mode of the VR controller without having to manually go through the menu in VR ? In the mean time, I will try different saved sessions and (remote) commands to try and solve the issue. If the demos are a success we will most likely make them available online so that anybody can try and improve them. Thank you in advance for your help. best, Lucien

2 4

semitransparent volumes with ambient occlusion
by Sindelar, Charles 03 Sep '19

03 Sep '19

Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward! Here is a little request. For the figures that I am now making for publications, I have a special interest in showing semitransparent molecular maps together with the corresponding models, with ambient occlusion lighting on. I think ambient occlusion makes this kind of figure much easier to interpret and more beautiful. What I have noticed is ambient occlusion seems to get automatically turned off as soon as a map becomes less than 100% opaque. I always assumed this was due to some kind of rendering difficulty. But then, I noticed that sometimes I can “trick” an old version of ChimeraX to do exactly what I want! Below is an example. Basically, in ChimeraX 0.6 I can set up everything just the way I want with an opaque map, then turn down the map opacity and get a nice, pretty figure just the way I like it. But then, as soon as I show/hide anything in the Model Panel, the ambient feature gets turned off! I noticed that in the most recent daily build, this “trick” no longer works and I can’t seem to ever get the pretty combination of transparent maps and ambient occlusion lighting that I like. I sure would like to have this option! I guess there must be some reason it is disabled? Best, Chuck Sindelar Opaque map + PDB (ChimX v0.6) (pretty but the PDB is obscured) [cid:image001.png@01D55FF9.D8266CF0] After adjust to 80% map opacity (ChimX v0.6) (pretty!) [cid:image002.png@01D55FF9.D8266CF0] After unshow/show PDB model (ChimX v0.6) (argh!) [cid:image003.png@01D55FF9.D8266CF0]

2 3

silhouette of transparent density
by YAO HE 31 Aug '19

31 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

5 10

silhouette of transparent density
by heyao 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

1 0

Chimera X and the Oculus Quest
by Thomas Gluick 28 Aug '19

28 Aug '19

HI First please excuse my computer language ignorance. My question is: Is the Oculus Quest compatible with Chimera X; if it is, is software available to link the program to the Quest. I am aware already that the Rift can be connected and also certain phones. Thank you for you time. Best Tom Dr. Thomas Gluick Assistant Professor of Chemistry School of Science and Technology 770-842-5532

2 1

Question about Calphas and line between them
by Yazan Abbas 21 Aug '19

21 Aug '19

Hi, While looking through the user guide, I came across an option to draw a line between consecutive Calphas that are displayed. I made a mental note to use that option in my figure, but I failed to bookmark it or write down what the command was. I've been through the user guide several times again, but can't seem to find it. Would appreciate it if someone could jog my memory. Thanks, Yazan

2 1

discontinuous helices in tube mode
by Yazan Abbas 19 Aug '19

19 Aug '19

Hi, Is there a parameter that can be changed to control how "cartoon style modeH tube" draws a continuous helix? In my model, most of my helices are broken up into 2-4 discontinuous helices (especially the long, curved ones). In pymol (cylinders mode) and chimera (pipes and planks depiction), the same helices are drawn as a single, continuous helix, suggesting that my model is ok. I tried adding a HELIX definition in the pdb file, and also tried forcing chimeraX to draw a helix using the setattr command, but neither strategy has helped. I also tried playing with the dssp energyCutoff with no success. Thanks, Yazan

2 3

Question about "color sample" command
by Sean Connell 19 Aug '19

19 Aug '19

Hello I have a question about the "color sample" command (Chimerax-daily version 0.91 2019-08-14) and its use in coloring a volume based on the values of a second volume (i.e. local resolution maps from relion) The command works great when I load the volumes in to chimerx but after I load them I want to transform them using matchmaker and the bring option so that all the volumes I want to view are in a common frame of reference. After I transform the volumes though if i re-issue the "color sample" command it seems to color the first volume according to the values in the un-transformed second volume I am guessing? Is this correct and expected or am I just doing something wrong? if this is what is happening is there a way to force color sample to read the transformed values or to re-sample the transformed maps so they are correctly read? Also the output of the color sample command reports the min,max and mean values, just to confirm this corresponds to the values of all the voxels displayed at the current threshold level right? Finally is there a way to show a key for the coloring in chimerax? Many thanks for any advice you can provide. Sean

3 3

Fly function in ChimeraX - 2
by Gabor PAPAI 16 Aug '19

16 Aug '19

Dear developers, I’ve seen that two years ago the fly command from Chimera was not implemented in ChimeraX. Is it implemented now? Or does ChimeraX have a similar function? I tried the view command inside the perframe function, unfortunately this didn’t result in a smooth transition between two named views. The only option I have now is to translate, zoom and rotate the scene with the individual commands, however this is quite tedious to set. Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 1

RESMAP output superposition.
by chimerax-announce-owner＠cgl.ucsf.edu 15 Aug '19

15 Aug '19

From: Shahid Khan <outlook_CD0472DE47DC92D6(a)outlook.com <mailto:outlook_CD0472DE47DC92D6@outlook.com>> Subject: RESMAP output superposition. Date: August 14, 2019 at 7:33:59 PM PDT Hello The python script for mapping the RESMAP local resolution output does not work in ChimeraX. Has anybody modified it so that it does? Or written a new script with the same purpose for ChimeraX. Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Understanding the output of the align command
by Yazan Abbas 14 Aug '19

14 Aug '19

Hi, I am trying to make a movie to rotate density in a manner that follows rotation between two atomic coordinates. To do that, I am aligning the two models and using the reportMatrix output to inform turn and move commands in order to transform the density. However, I am encountering some difficulty, and I'm not sure if this is related to bugs or my lack of understanding. For example, if I want to move from the position of model #1 to model #2, "align #1/b toAtoms #2/b move nothing reportMatrix true" produces the following: *Axis 0.11 -0.018 0.99Axis point 166 190 0Rotation angle (degrees) 108Shift along axis -0.24* I would think my turn command should be *turn 0.11,-0.018,0.99 108 models #1 center 166,190,0* But that doesn't work. I can get it to work if I assume that the reported axis is x,z,y instead of the expected x,y,z. Also, I have to use a rotation angle of -108 instead of 108. I'm not sure if I am using the axis point value correctly though, is it correct to use that as my center of rotation? It's location (166, 190, 0) places at the top of the box, which seems unusual to me. And finally, would I use this same information in a move command (i.e. move axis distance(shift), as reported by the align command? Many thanks in advance, I hope explained this clearly. Best, Yazan

3 5

Morphing atomic models and volumes in a single movie
by Yazan Abbas 05 Aug '19

05 Aug '19

Hi, I am trying to create a movie that is morphing between 3 atomic models while simultaneously morphing between the 3 corresponding volumes. The following is my script for recording this movie: *set max 25windowsize 1080 1080view frame1movie record supersample 3wait 1volume morph #12,13,14,15 frames 181 playStep 0.005524861878453038 constantVolume true modelId #16perframe "surface dust #16 size 40" frames 181coordset #10 1,181wait 181movie stopmovie encode test_full.mp4 quality high* There are 4 maps in my morph, but the fourth map is simply a copy of the first in order to mimic the *wrap true* option of the atomic model morph. I am encountering the following issue during the volume morph step: somewhere in between the morph between volume #14 and #15, the map disappears for a fraction of a second in the movie. I suspect its because of a calculation/waiting issue, because if I record the movie using filtered versions of the volumes (*volume guassian sDev 2*), I don't have the same issue. Am I correct in my interpretation of the issue? Is there a way to modify my recording script to avoid this? Thanks, Yazan

2 1

pixel size
by Yazan Abbas 01 Aug '19

01 Aug '19

Hi, I am trying to create a scale bar using the following method: 1. camera is set to ortho 2. save image image.png width 4000 height 4000 transparentBackground true 3. check pixel size in chimeraX using the zoom command (which shows Pixel size at center of rotation is 0.178) 4. in imageJ, set the scale to be 0.178Å/pixel which turns into 5.618 pixels/Å 5. Show scale bar of desired in length in ImageJ However, the resulting scale bar looks unusually small given the dimensions of my particle. Have I misunderstood something about the pixelSize settings? The user guide doesn't say anything about pixelSize when one of or both of width and height are specified in the same image command, so I assumed the pixel size of the saved image would be the same as in the graphics window. Thanks, Yazan

2 3

Runing multiple command lines in ChimeraX
by Marie Locard-Paulet 26 Jul '19

26 Jul '19

Hello, I am running ChimeraX version 0.9 (2019-02-16) on a Mac (macOS Mojave version 10.14.6). It works fine, and I can work by adding commandes in the command “box” in the bottom. But I would like to open a text file with multiple ChimeraX command lines (for reproducibility and gain of time). I saw the command “open” that should open a document with the suffix “.com” or “.cmd”. It doesn’t work in my hands. It says it does not recognise the suffix. Is there something I am missing? Could you please help? Kind regards, Marie. --------------------------- Marie Locard-Paulet NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen, Denmark

2 1

ChimeraX Side View
by Elaine Meng 19 Jul '19

19 Jul '19

In response to a question about Side View... From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Side View Date: July 19, 2019 at 10:34:44 AM PDT Hi Zhijie, Thanks for your registration comments! You will be happy to know that ChimeraX does have Side View. You can choose it from the menu: Tools… General. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html> To make a tool (Side View, etc.) start automatically every time you start ChimeraX, right-click in that tool (or Ctrl-click on some systems) to show the context menu, and from that menu choose “Start at ChimeraX Startup” <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#tool-context>

1 0

Zalman 3D monitor support
by Tom Goddard 19 Jul '19

19 Jul '19

Hi Zhijie, We are not likely to support Zalman 3D monitors (row interleaved stereo mode) in ChimeraX. Those monitors were made 2009-2011 and then discontinued. We don't have the funding to support technology from long ago. Tom

1 0

Fw: Genentech ChimeraX source code inquiry
by Williams, Joanne 18 Jul '19

18 Jul '19

________________________________ From: Slaton Lipscomb <lipscomb.slaton(a)gene.com> Sent: Thursday, July 18, 2019 10:00 AM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Genentech ChimeraX source code inquiry Hi, Genentech has a commercial license for ChimeraX. However we have run into challenges installing it for our high performance computing cluster because of the binary-only distribution model. We automate the build and deployment of applications for our HPC cluster using the tool EasyBuild. It's far easier to do this when working from source code. Is the source code for ChimeraX available to license holders? thanks slaton -- Slaton Lipscomb gRED IT Scientific Computing Support for gRED IT Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…> FAQs for gRED Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…>

1 0

Molecular Dynamics Viewer
by James Starlight 16 Jul '19

16 Jul '19

Dear ChimeraX users! I would like to make a movie of molecular dynamics trajectory that has been pre-converted to pdb format (totally 250 frames). 1) Firstly, I have a problem with the recognition of the SS elements of that ensemble in ChimeraX, where each snapshot looks just like a mixture of points ( i tried to use dssp but it did not solve the issue). At the same time the snapshots looks fine in another viewers including UCSF Chimera (not X) 2) If I have a pdb of the same protein with mapped B-factors and then I colored it using color byattribute bfactor palette rainbow range 2,100 2) would it be possible to map the trajectory to that pdb in order to see the motions (observed in MD) mapped onto the structure that has been coloured by b-factors? Thanks for help!

3 15

session files do not save "color zone" command actions
by Rasmus Kock Flygaard 15 Jul '19

15 Jul '19

Hi all, I'm using chimerax-daily-build (downloaded two weeks ago, Chimerax-0.91). I am using a model to color EM density maps per subunit using the "color zone ..." command, but when I save Chimerax session files these colored zones are not saved and I have to redo all of them to fully restore a session. Is there any way to include these colored zones in the saved sessions files? Kind regards, Rasmus ------------------------------------ Rasmus Kock Flygaard, Ph.D Postdoc, Amunts' Lab SciLifeLab, Stockholms University Sweden

2 1

MLP value of the ASP and GLU carboxylate
by Zhijie Li 13 Jul '19

13 Jul '19

Hello, I noticed that the lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py: 'ASP': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CG': 0.54, 'N': -0.44, 'O': -0.68, 'OD1': -0.68, 'OD2': 0.53} 'GLU': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CD': -0.54, 'CG': 0.45, 'N': -0.44, 'O': -0.68, 'OE1': -0.68, 'OE2': 0.53}, As as result the hydrophobic surface representation always show hydrophobic patchs on the carboxylates, which look quite odd to me. Is there a justification for this setting? In addition, aren't the two oxygens in the carboxylate equal considerting that they are in resonance? Zhijie

3 5

mesh lineThickness
by Yazan Abbas 12 Jul '19

12 Jul '19

Hi, In chimera the volume mesh lineThickness option could be changed. I can't seem to find the equivalent option in chimeraX. Is it possible to change the thickness of mesh lines? Thanks, Yazan PS apologies if you received this message twice, there was an error in my browser when first sent...

2 2

WebGL apps still in the pipeline?
by Oliver Clarke 11 Jul '19

11 Jul '19

Hi, Loving the regular improvements to ChimeraX! Just wondering regarding a web viewer - the original roadmap for chimeraX mentioned “WebGL apps” (http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html <http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html>), and original Chimera had a limited capacity to export scenes as interactive html files. Is this still something that is in the pipeline for ChimeraX? I would really love to be able to export ChimeraX scenes in a format that I can share on the web, without the need for users to download and know how to use ChimeraX. Ideally the user would be able to rotate, zoom and slab, but perhaps not translate - that is, the center of rotation would be fixed. The idea would be to enable sharing of “interactive figure” kind of views of the molecule/map (perhaps allowing switching between multiple scenes/views within one session). Cheers Oli

2 1

Appearance of thick edges
by Yazan Abbas 11 Jul '19

11 Jul '19

Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug? I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan

3 5

feature request / suggestion
by Alexis Rohou 10 Jul '19

10 Jul '19

Hello, Apologies if this already exists, but I'd like to suggest a new option to the show/hide command: show /spec/ toggle which would behave like the toggle option of volume (one of my favorite chimeraX features by far), but would work on atomic models. Within the spec, anything currently shown would become hidden, and vice versa. Cheers, Alexis

3 3

Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by James Starlight 08 Jul '19

08 Jul '19

Hi Greg, sorry for some delay :-) Actually I just checked and indeed, there is still problem with rendering of the images with chimera-X using here is the detailed output if it would help chimerax-daily --offscreen --nogui "${output}/!temp/chimeraX.${pdb_name}.cxc" INFO: Offscreen rendering is not available. INFO: module 'OpenGL.osmesa' has no attribute 'OSMESA_DEPTH_BITS' INFO: UCSF ChimeraX version: 0.9 (2019-04-03) INFO: © 2016-2019 Regents of the University of California. All rights reserved. INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/chimeraX.0476.cxc INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb INFO: Summary of feedback from opening /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb --- _warning_ | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX INFO: _B-factors_0476.pdb_ title: **Gallium Rubidium Oxygen Manganese Argon Carbon Silicon** [[more info...]](cxcmd:log metadata #1) INFO: Chain information for B-factors_0476.pdb #1 --- Chain | Description [ ](cxcmd:select :1-219 "Select chain") | [No description available](cxcmd:sequence chain #1/ "Show sequence") INFO: Executing: open /home_pers/novikov/Bureau/test/test/florence.pdb INFO: Chain information for florence.pdb #2 --- Chain | Description [ ](cxcmd:select #2:1-219 "Select chain") | [No description available](cxcmd:sequence chain #2/ "Show sequence") INFO: Executing: mmaker #1 to #2 INFO: Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 INFO: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: INFO: Executing: hide #2 models INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: dssp #1 INFO: Executing: zoom 1.3 ERROR: turn x 15 y 15 z -40 ERROR: ..........^ ERROR: Expected an integer >= 1 or a keyword ERROR: Expected an integer >= 1 or a keyword INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: preset "'overall look'" publication INFO: Preset expands to these ChimeraX commands: _set bg white; set silhouettes t_ INFO: Executing: set silhouettes true INFO: Executing: set silhouetteColor indigo INFO: Executing: set silhouetteDepthJump 0.02 INFO: Executing: color byattribute bfactor palette rainbow range 2,100 INFO: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 STATUS: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 INFO: Executing: cartoon style width 2.4 thickness 0.50 xsection barbell INFO: Executing: 2dlabels create title text '"Cluster 0476"' color red font gothic xpos .01 ypos .90 size 36 INFO: Executing: lighting depthCueStart .4 depthCueEnd .8 INFO: Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer INFO: Executing: save image /home_pers/novikov/Bureau/test/test/!plots/visu_0476.png format png width 600 height 600 supersample 4 transparentBackground false and this is my script open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0472.pdb open /home_pers/novikov/Bureau/test/test/florence.pdb mm #1 to #2 hide #2 models wait dssp #1 #view zoom 1.3 turn x 15 y 15 z -40 wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 color byattribute bfactor palette rainbow range 2,100 cartoon style width 2.4 thickness 0.50 xsection barbell # make info of the screen 2dlab create title text "Cluster 0472" color red font gothic xpos .01 ypos .90 size 36 # options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer save image /home_pers/novikov/Bureau/test/test/!plots/visu_0472.png format png width 600 height 600 supersample 4 transparentBackground false exit пн, 22 апр. 2019 г. в 23:38, Greg Couch <gregc(a)cgl.ucsf.edu>: > > Salut, > > Does ChimeraX work in offscreen mode for you now? I believe it is fixed. > > -- Greg >

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Re: [chimerax-users] [Chimera-users] Cylinder coloring extension
by Elaine Meng 03 Jul '19

03 Jul '19

Hi Thomas, Chimera “pipes” are always a single color each. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pi…> However, our new program ChimeraX has a cylinder-helix representation in which each residue’s segment can be a different color. Like Chimera, ChimeraX is a free download for noncommercial use. Commands are similar but not identical between the two programs. <http://www.rbvi.ucsf.edu/chimerax/index.html> In ChimeraX, if I open 2gbp and from the menu apply preset “cylinders/stubs” and then preset “publication” I get this: ... and then command “color by bfactor palette rainbow” gives this: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 3, 2019, at 3:48 AM, Thomas Marcellino <marcellino.tom(a)gmail.com> wrote: > > Dear Chimera Team, > > I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? > > Looking forward to an answer, > Thank you for your time reading my suggestion. > > Thomas M

1 0

mclip - surface clipping per-model
by bertrand beckert 03 Jul '19

03 Jul '19

Hi Elaine, I just wonder if the option clipping per-model has also been introduced in ChimeraX like it is in chimera ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mod…) ? Apparently the command mclip doesn't seem to exist... Has it been replaced? Best Bertrand

2 1

MacOS two-finger swipe on help window
by Alexis Rohou 03 Jul '19

03 Jul '19

Hi all, Not sure this is a bug, but on my MacOS laptop when I use two finger swipe motion while hovering over the help window (to browse up and down the page), the help page is scrolled as expected, but simultaneously the view in the main window is rotated. Is this expected behavior? It seems a bit counter productive to me. Cheers, Alexis

2 3

color a surface by volume data
by bertrand beckert 02 Jul '19

02 Jul '19

Dear all, I have been searching in the documentation for quite a while and I haven t yet found the solution of how we can in chimeraX color a surface/volume by a volume data like in chimera ... i.e: local resolution map in cryo-em... in chimera: volume viewer/Tools/Surface color/color suface by is it possible to do so in ChimeraX? Any Help would be really appreciated! Thanks also for the amazing software ! Best Bertrand

2 1

An error opening chimerax seesion
by Yehuda Halfon 02 Jul '19

02 Jul '19

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

2 4

Placing markers using the VR wands
by Schmid, Michael F. 01 Jul '19

01 Jul '19

Hi- I don’t seem to be able to activate the Marker Placement functions in the menu that it called up by pushing the menu button (above the trackpad of the wand) to display a floating menu. It doesn’t seem to work with “vr off” either, using the mouse. I’d like to place markers in a tomogram, either in a density, or (preferably) at a specific 3D position with the wand. Thanks, Mike Schmid

3 4

suggestion for ChimeraX on MacOS
by Alexis Rohou 01 Jul '19

01 Jul '19

Hi there, I noticed that when I do "open browse", the native MacOS file browser is started, but when I click on File > Save..., a file browser from some other toolkit is used. I find this inconvenient because that file browser does not know about my recent history, bookmarks, etc. Any chance the File > Save... dialog could use the native OS file browser? Cheers, Alexis

2 1

Restoring views and how to use clip
by Yazan Abbas 01 Jul '19

01 Jul '19

Hi, Instead of using chimera sessions (which can get very big) to save my work when preparing figures for publications, I save all my commands in a .cxc file to be read by chimeraX later. Is there a single command that outputs all the necessary information in an appropriate format needed to restore a view? Currently what I have done is *alias myview view matrix; zoom *to output the information into the log, but the output needs to be re-formatted whenever I want to use that information with the view matrix and zoom commands. Is there a command that outputs that information in a format ready for copying and pasting? I know name view can partially fulfil what I am looking for, but it is only session specific. On a related note, I want to also restore the clipping for each figure/panel I create, but I don't seem to be using the clip command appropriately. For example, if I enter the command clip list, and the output is Using 2 clip planes: far -34.697, near -45.723, executing the command clip far -34.697 near -45.723 does not restore the same view. Am I missing something? Thanks, Yazan

3 2

Orientation and pre-superimposition of the PDB
by James Starlight 28 Jun '19

28 Jun '19

Dear Chimera Users! I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation). The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!) Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX! Thanks in advance!

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Mouse modes
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, Apologies if this has been posted before, still new to chimerax and the mailing list. Was wondering if there are plans to add support for modifying mouse keys with ctrl (similar to what is in chimera). I am also wondering if there are plans to create a recenter + change pivot button/function that is also part of chimera. Thanks, Yazan

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Map issue after using color zone
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, I already submitted a bug report for this issue, but was wondering if there was a quick fix. After applying color zone to my map, parts of it appear broken where density is forming protrusion. An image example is attached. Using the latest daily build (jun 25). Thanks, Yazan

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volume splitbyzone and color zone issues
by Yazan Abbas 26 Jun '19

26 Jun '19

Hi, I executed 'color zone #2 near #1 distance 5 sharpEdges true' to colour a map I loaded, followed by "volume splitbyzone #2', but repeatedly would get an error that the volume specified is not coloured by zone. Eventually after trying multiple times, it worked, however the log outputted the following: Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py", > line 130, in invoke > return self._func(self._name, data) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 3557, in _update_drawings > v.update_drawings() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 701, in update_drawings > self._update_surfaces() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 724, in _update_surfaces > s.update_surface(ro) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 1953, in update_surface > va, na, ta, hidden_edges = self._calculate_contour_surface(matrix, > level, rendering_options) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2048, in _calculate_contour_surface > rendering_options, level) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) > ValueError: not enough values to unpack (expected 3, got 2) > Error processing trigger "graphics update": not enough values to unpack > (expected 3, got 2): > ValueError: not enough values to unpack (expected 3, got 2) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) I also get the following when using the color zone command, even though color zone works (most of the times, sometimes it fails) Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", > line 254, in execute > cmd.run(cmd_text) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", > line 2641, in run > result = ci.function(session, **kw_args) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/std_commands/color.py", > line 1248, in color_zone > color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges, > auto_update = update) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 14, in color_zone > zc.set_vertex_colors() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 84, in set_vertex_colors > replace = True) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 123, in color_zone_sharp_edges > ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 147, in _edge_cuts > f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, > distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f) > ValueError: Cut fraction 1.8061 is out of range (0,1) > ValueError: Cut fraction 1.8061 is out of range (0,1) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)

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Distinguishing between upper and lower case chain IDs before and after splitting chains
by Yazan Abbas 25 Jun '19

25 Jun '19

Hi, My model (cif format) contains 34 chains, and so I've been using upper case and lower case letters for chain IDs. When I read in my model, the select command distinguishes between upper case and lower case, but after applying the split command on my model ('split #1 chains'), the select command no longer distinguishes between upper and lower case. I.e. 'select #1/D' will select both chains D and d. The split command works correctly, producing models 1.1-1.34. Also, is it possible to create a model from a selection? I can't find such a command anywhere, and the only thing I can figure out is to do the following: 'save *name* format mmcif models *selecion_name*; open test.cif' Thanks, Yazan

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measure blob - persistent color?
by Alexis Rohou 25 Jun '19

25 Jun '19

Hi there, I absolutely love the new measure blob UI in the daily builds. Very useful. Thank you so much for putting it together. Is there a way to get the blob surface color to persist beyond hiding/showing the volume object? Obviously, in a script I could just re-measure the blob and re-color it, but is there another way to make the color "stick"? (Note, I don't plan to change the isocontour level) Cheers, Alexis

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#2013: Trouble pip-installing Pyyaml prereq for bundle
by Andrés Giner Antón 20 Jun '19

20 Jun '19

Hello, two weeks ago we reported a problem regarding the installation of Pyyaml as a prereq of a bundle that we created, do you have any forecast of when we will get an answer? Here is the URL of the ticket: https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2013 Thanks for your attention. Greetings, Andrés Giner Antón

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ISOLDE 1.0b3 now released for ChimeraX 0.9
by Tristan Croll 17 Jun '19

17 Jun '19

Dear ChimeraX users, Just letting you know that I've released ISOLDE 1.0b3 on the ChimeraX Tool Shed for use with ChimeraX 0.9. If you're not familiar with ISOLDE, you can get an overview at https://isolde.cimr.cam.ac.uk/. In brief, ISOLDE is designed to allow the high-fidelity, interactive remodelling/refinement of atomic models into low-medium resolution cryo-EM or crystallographic electron density maps. In designing ISOLDE, I've always had two groups in mind. The first is, of course, the experimental structural biologists whose job it is to solve the structures of new macromolecules and their complexes. The second (and, to my mind, equally important) group is the downstream *users* of such models. Like every other human endeavour, macromolecular model building is an imperfect field, and (particularly in the worse-than-2-Angstrom resolution range targeted by ISOLDE) many deposited models contain serious errors that are eminently fixable with modern tools. My hope is that ISOLDE will become a useful tool allowing you to directly inspect your model of interest in the context of its original data, providing you with a feasible pathway towards fixing any issues you find (or, failing that, moving to a new target) prior to committing serious resources to its study. Please enjoy. Constructive feedback is always welcome. Best regards, Tristan

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Transparent background movie
by Norberto Escudero 14 Jun '19

14 Jun '19

Hi, I have succesfully created images with transparent background, but it seems is an impossible task for a movie. Is there any way around this? Thanks and regards, -- Dr Norberto Escudero Urquijo Prof. A. Warren's group Cambridge Institute for Medical Research (CIMR) Hills Road, Cambridge, CB2 0XY

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