- ChimeraX-users - RBVI Mailing Lists

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

3 2

Volume series
by Kotaro TANAKA 08 Jun '20

08 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

4 7

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.

2 1

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

2 2

developing bundles autocompletion
by Daniel Esteban Palma Igor 05 Jun '20

05 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

2 3

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]

3 2

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

1 0

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

2 2

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

2 2

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>

2 3

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

2 1

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/>

5 6

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

2 1

Feature suggestion - show color code in picker?
by Oliver Clarke 19 May '20

19 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

3 4

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> ##################################

2 1

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

3 4

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

1 0

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

1 0

Stereo and VR support
by Gökhan Tolun 13 May '20

13 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

3 3

pyqtchart
by Anthony James Schaefer 13 May '20

13 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

2 3

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>

2 1

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>*

2 1

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

2 1

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

3 3

Map "Blobs" tool - Generate objects?
by Christophe Leterrier 11 May '20

11 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

4 5