- ChimeraX-users - RBVI Mailing Lists

Fwd: tile command in chimeraX
by Elaine Meng 20 May '19

20 May '19

> > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] tile command in chimeraX > Date: May 20, 2019 at 10:25:27 AM PDT > To: françois SERRA <serra.francois(a)gmail.com> > Reply-To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > > Hi Francois, > Not a dumb question, but sorry, there is no “tile” equivalent in ChimeraX currently. If you don’t have too many structures, you could first superimpose them all in the middle, zoom out somewhat (“zoom” command) and then translate them individually up/down (y axis) and left/right (x axis) with the “move” command, but it would be a little tedious and require some trial and error as to spacing. It may be useful to save/restore positions with the “view” command. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > 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 20, 2019, at 3:17 AM, françois SERRA <serra.francois(a)gmail.com> wrote: >> >> Hi, >> sorry for the stupid question, but I spent quite some time searching for it. >> Is there some alternative to the "tile" command in chimera X? >> thanks! >> great tool :) >> francois >

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tile command in chimeraX
by françois SERRA 20 May '19

20 May '19

Hi, sorry for the stupid question, but I spent quite some time searching for it. Is there some alternative to the "tile" command in chimera X? thanks! great tool :) francois -- François Serra *senior researcher - comparative epigenomics* Computational Biology Group - Barcelona Supercomputing Center (BSC) C/ Jordi Girona, 29 08034 Barcelona Tel: +34 934 137 97

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smoothen coils
by Gabor PAPAI 13 May '19

13 May '19

Dear developers, I would like to show helices as tubes (this I know how to do) and coils between them with smooth trajectories, more schematic, as it is drawn in Chimera using Pipes and Planks (or even more). I would appreciate your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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Feature Request: Dust ranges and new object as output
by Scott, Brandon L. 30 Apr '19

30 Apr '19

We can currently remove objects of a given size; it seems like it would be fairly straightforward to allow a range of object sizes to be kept from the middle, i.e. remove objects less than 20 and greater than 1000. Additionally, it would be really helpful if we could output the 'dusted' components as a new model so they could be individually colored and displayed, or be able to access the measured sizes of the objects for further analysis. Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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morph with molecular surface for part of molecule
by Susan Lea 30 Apr '19

30 Apr '19

How can I generate a morph with a molecular surface representation? many thanks Susan Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege

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Some preferences will reset
by Eric Pettersen 25 Apr '19

25 Apr '19

Hi all, In order to improve the modularity and maintainability of the ChimeraX code, the way some settings/preferences were handled was changed so that the code for that setting/preference could be kept in the appropriate tool bundle rather than in the ChimeraX core. A consequence of this change is that for settings/preferences that moved, they will revert to their initial default values rather than any values you may have saved for them. This will only happen for builds later than today, and furthermore if you go back to an older build it will still have your old values. For most settings/preferences this is not a big deal — you can easily just change them and save them again. The one setting that may be a little tricky is the “Startup commands” setting since there might be a lot of text saved in that one. Nonetheless, as long as you don’t delete your old build you can just start that and copy the commands from that into the new build. The preference categories that got moved are: Clipping Distances Labels Log Startup Trackpad Window —Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX python crush in no-gui mode
by James Starlight 16 Apr '19

16 Apr '19

Dear ChimeraX users! I am using a cxc script together with the following options to run ChimeraX in no-gui mode. chimerax-daily --offscreen --nogui test.cxc here is my scrript # chimeraX script windowsize 800 600 open ./test.pdb view; zoom 1.0; turn x 90; turn z -80; preset 'overall look' publication color byattribute bfactor palette rainbow range 2,100 # make info 2dlab create title text "B-factors for" color red font gothic xpos .04 ypos .90 size 30 # options for light light depthcuestart .4 depthcueend .8; lighting full save image ./test.png format png width 800 height 600 supersample 4 transparentBackground false This script works fine with GUI producing very good picture but with the --nogui it gave me error: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py", line 699, in init commands.run(sess, 'open %s' % arg) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw return f(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py", line 601, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 467, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 421, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/scripting.py", line 115, in open_command_script run(session, text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 203, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/image.py", line 43, in save_image raise LimitationError("Unable to render images to save them") chimerax.core.errors.LimitationError: Unable to render images to save them could you help me how it may be fixed? Thank you in advance! Gleb

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Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by Elaine Meng 15 Apr '19

15 Apr '19

Hi James, There is a different email address for asking ChimeraX questions (CC’d here). Yes, you can script imaging in ChimeraX with nogui if you are using Linux and start with the “nogui” and “offscreen” options on the system command line (they have dash-dash in front but my Mail keeps editing it to a long hyphen instead). <http://rbvi.ucsf.edu/chimerax/docs/user/options.html> In ChimeraX the command script filenames end in .cxc <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> The commands may be different than in Chimera. Open is with “open” save is with “save” and there is no publication preset but you can change to white background and show silhouettes with the “set” command. See the individual command help pages <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> making images <http://rbvi.ucsf.edu/chimerax/docs/user/images.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 Apr 15, 2019, at 2:14 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: > > Dear Chimera users! > > Would be possible to use new ChimeraX for execution of some simple > scripts for structure visualisation and imaging via no-gui mode? > > I am using bash script to loop over pdbs and would like to > > 1) open each pdb which contains b-factors info in chimeraX > 2) apply preset publication > 3) colour the pdb using "color byattribute bfactor palette rainbow ave residue" > 4) save high quality image at the selected directory using chimera render > > Would it be possible to do these things directly from linux terminal > providing each time pdb and some script file with the list of the > applied commands? > > chimerax-daily ${pdb} ${script} > > Thank you in advance!

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Dome projection camera mode
by Tibor Füzik 10 Apr '19

10 Apr '19

Dear ChimeraX developers, I have not found the "dome" projection camera mode in ChimeraX (as it is in Chimera). Is there any equivalent projection (camera mode) or a workaround to get it? Would it be hard to implement it ChimeraX? Thanks. All the best, Tibor

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PDBe-KB ligand centric pages survey
by Lukas Pravda 04 Apr '19

04 Apr '19

Dear ChimeraX users, We are in the process of redesigning the ligand pages of PDBe and we would be grateful if you could fill out a short survey to help us understand what information about small molecules / ligands you would find useful. The survey is available at https://bit.ly/2FFmHFG. Recently, we have introduced protein-specific aggregated views on the structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in Europe Knowledge Base (PDBe-KB). We highlight the available information related to structures of specific proteins, including structural and functional annotations, domains, ligand-binding sites and interfaces. In the next step we would like to present a similar aggregated view from a small molecule / ligand perspective. Thank you for your time, Lukas -- Lukas Pravda, Ph.D. Bioinformatician/Scientific Programmer Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD United Kingdom

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Feature request: save cxc
by Zack Gainsforth 02 Apr '19

02 Apr '19

Hi, I am finding that saving my visualization as a cxc (scripting command) file leads to good reproducibility. Often, when I save a session (cxs) file, it doesn’t open again later (I think because directory path names change), but if I produce the visualization by coding a cxc file instead, then it hasn’t failed (yet!). In addition, I want to keep track of actions such as median filters, and filter parameters, pixel scaling, all that jazz. When I code this into a cxc file, all that info is in the code record. When I save a session file I often cannot find that information again later (was it a gaussian filter? median? What do I write in the paper!?) I would suggest a feature to save a cxc file or output a journal of all changes for a cxs file so I can see what I did at least for documentation/reproducability later. Cheers, Zack

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Re: [chimerax-users] Output motion prickle magnitude
by Scott, Brandon L. 02 Apr '19

02 Apr '19

Based on previous correspondence I added an output option in motion.py. Is there anyway to do a pull request or something similar, so that I don't have to make the changes everytime I stay up to date with the nightly builds? Thanks, -Brandon

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Transparency bugs with ribbons and density maps
by Pascal Albanese 27 Mar '19

27 Mar '19

Dear all, I'm haviong troubles with visualization of trasnparencies when using EM maps and PDBs. See in the example here: [image: image.png] The ribbon in the front is completely transparent (with silhouettes), the surface is set with a 50% transparency, and the pseudobonds inside or behind can be only visible when transparency of pbonds is set to 0 (at 5 already they disappear). Does anyone already experience these issues? Bests, Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

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Coulombic surface coloring
by Gabor PAPAI 27 Mar '19

27 Mar '19

Dear ChimeraX team, I would like to color a protein surface by electrostatic potential. Is there a way in ChimeraX to do that? My protein is too large (more than 20 000 atoms) to create a surface in Chimera, but ChimeraX has no problem to create it. Thank you in advance for your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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Implement Crosslinks/pseudobond/distances subselections and/or export
by Pascal Albanese 22 Mar '19

22 Mar '19

Dear ChimearX Users and developers, I'm using ChimeraX for visualization and analysis of pseudobonds datasets from Crosslinking-MS and i found new features very useful (min max selection etc). I think it would be useful (but i don't know how much effort will be required) to be able to select subsets of distances (e.g. form 15 to 24 Angstroms, or involving chain A and B) and being able to create and export these subsets. for instance i have a Complex of A, B and C and i want to select all pseudo-bonds involving A and B and export them as pb file (to be able to load them as a separate model lateron). Or to sel min 15 max 24, and then export them as pb file (with "save" function). I think it would be really useful for both crosslinks visualization and analysis (i work with datasets of thousands of crosslinks on big complexes which make difficult to subselect them, i have to do it with pymol, then generate subsets and reformat them as .pb files). i had a look to previous threads, but i didn't found similar topics. If i'm wrong my apologize. Thank you! Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

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Re: [chimerax-users] [Chimera-users] color key in chimera X
by Elaine Meng 18 Mar '19

18 Mar '19

Hi Pranav, ChimeraX does not yet have color-key drawing, sorry. One possibility for now is that even if you want to make the main image in ChimeraX, you could still make the color key separately in Chimera and then combine them in some image-editing program like Photoshop. In Chimera, you could use the “colorkey” command as Ibrahim suggests, or the GUI (Tools… Utilities… Color Key). Either way you would have to define the colors and set values “manually” to match the coloring in ChimeraX, so we understand it is not as convenient as when the image and key are in the same program. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> There is also a ChimeraX e-mail list chimerax-users(a)cgl.ucsf.edu that you can use if you have other issues/questions about ChimeraX specifically. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 18, 2019, at 12:13 PM, Moustafa, Ibrahim M. <ria2(a)psu.edu> wrote: > > Hi Pranav, > > Not sure about ChimeraX but in Chimera you can use 'colorkey' command line: > > colorkey x1,y1 x2,y2 value1 color1 value2 color2.... > > example: > colorkey 0.1,0.1 0.11,0.5 3.0 blue 4.0 cyan 5.0 green 6.0 yellow 7.0 orange 8.0 red > > You can use the colors and their values from the output of local resolution map. > > > Ibrahim > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of Pranav Shah <p.shah.lab(a)gmail.com> > Sent: Monday, March 18, 2019 2:56 PM > To: chimera-users(a)cgl.ucsf.edu BB > Subject: [Chimera-users] color key in chimera X > > Hi, > I have a isosurface rendering that I have colored by radius as well as > local resolution. I want to now place a colour key in the image to > indicate the relevance of the colors. Is there a way to achieve this > in ChimeraX? If not, is there a way to easily port the commands to > Chimera? > > Cheers, > Pranav > -- > Pranav Shah > Postdoctoral Research Fellow.

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Volume Rendering Issue
by Scott, Brandon L. 15 Mar '19

15 Mar '19

I am trying to set the thresholds to properly display volumetric fluorescence data, and for some reason, when viewed from the side, i.e. xz or yz projection, the volume goes black. I've attached two images (top view and side view) with not changes to anything else by positioning, and this can be seen clearly in the rotation video I attached. I guess my question is, is this a bug, or is it acting as it was intended? Thanks for the help, -Brandon [cid:1b1e95a3-2efc-477f-925e-74b92b367f68] [cid:56f70b34-d199-466f-a578-76fde802d5ec] ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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OpenGL error running ChimeraX under VNC on CentOS 7
by Tom Goddard 14 Mar '19

14 Mar '19

Hi Alexis, ChimeraX is crashing in the OpenGL graphics driver (libGL.so.1) when the Qt window toolkit is trying to use it. This is certainly an OpenGL graphics problem with your VNC setup. Sometimes VNC is run mirroring an actual display connected to the server computer you are connecting to, and sometimes it displays a virtual desktop, for example, when connecting to a server that has no physical display. ChimeraX will very likely work if VNC is mirroring an actual display on the server, but will almost surely fail if it is using a virtual desktop on the server. This is because OpenGL rendering only works to a physical display directly connected to the computer running the app (ChimeraX). I think there have been efforts to send the OpenGL commands to another computer and have that client computer's graphics card render, but that is a very obscure capability, and I have only heard of it failing, never saw it work. Tom > On Mar 14, 2019, at 10:40 AM, Alexis Rohou wrote: > > Hi Tom, > > I am attempting to get ChimeraX running on a CentOS7 workstation with a > nice discrete GPU card for running ISOLDE. Unfortunately, I am having no > luck so far. Tristan Croll, who is helping me get started with ISOLDE, > suggested I send you directly this report and ask for guidance. > > Some details: > - I installed the daily CentOS7 RPM from yesterday (13-March-2019) > - I am connecting to this workstation using a VNC server/client. I do > not have physical access to the workstation, at least not any time soon > - Starting the binary under gdb gives the error & stack trace copied below > - it could be that this is just related to OpenGL over VNC not working > properly. If you suspect this is true, could you suggest some test I > could run to confirm this is the case? > > Any other hints would be most welcome! > > Thanks, > Alexis > > >> WARNING: QOpenGLShader::compile(Vertex): failed >> WARNING: QOpenGLShader::compile(Fragment): failed >> WARNING: Could not link shader program: >> "" >> >> Program received signal SIGSEGV, Segmentation fault. >> 0x00007fffe6e6a013 in ?? () from /usr/lib64/nvidia/libGL.so.1 >> Missing separate debuginfos, use: debuginfo-install >> ucsf-chimerax-daily-2019.03.13-1.el7.x86_64 >> (gdb) bt >> #0 0x00007fffe6e6a013 in () at /usr/lib64/nvidia/libGL.so.1 >> #1 0x00007fffe54e268a in () at >> /usr/lib64/nvidia/libnvidia-glcore.so.340.107 >> #2 0x00007fffe6eac1a0 in () at /usr/lib64/nvidia/libGL.so.1 >> #3 0x00007fffe0e4fc6f in () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 >> #4 0x00007fffe0df1842 in () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 >> #5 0x00007fffe0df2143 in >> QPlatformBackingStore::composeAndFlush(QWindow*, QRegion const&, >> QPoint const&, QPlatformTextureList*, QOpenGLContext*, bool) () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 > > >

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MOL2 import
by Marco J. Müller 14 Mar '19

14 Mar '19

Dear ChimeraX Team, when I try to load structure outputs of docking runs in .mol2 format into ChimeraX, it fails to load them, while the same can be imported by Chimera successfully. After a bit of playing around I found that the following section is relevant and fails in this format: @<TRIPOS>MOLECULE MYCOOLMOLECULE 57 62 1 SMALL USER_CHARGES The problem seems to be that ChimeraX requires explicit definitions of /#features/ and/#sets/ in the third line (apart from /#atoms #bonds #substructures/), while they are typically omitted in most programs. So the following lines could be imported: @<TRIPOS>MOLECULE MYCOOLMOLECULE 57 62 1 0 0 SMALL USER_CHARGES Can this case be addressed in a future version of ChimeraX? Thank you in advance, Marco -- Marco J. Müller PhD student Technische Universität Braunschweig Institute of Medicinal and Pharmaceutical Chemistry https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany

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How can I use command crosslinks with bonds?
by Jun Ha Song 04 Mar '19

04 Mar '19

Dear RBVI, I want to use few command lines that are exclusively available for pseudobonds. The problem is that my model is consisted of markers and links, and there seems like no possible way for me to simply transfer bonds into pseudobonds. What commands like *crosslinks histogram *provide seems way to good for it to be limited for pseudobonds only. Is there a technical reason why such command is only applicable with pseudobonds? Can commands in Chimera/ChimeraX that work with pseudobonds easily be adapted to work with bonds, or is that too much of technical difficulty? If it is not feasible, is there a way to turn bonds into pseudobonds? Best, Junha Song.

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matchmaker RMSD in ChimeraX
by Tom Goddard 04 Mar '19

04 Mar '19

> From: Martin Moncrieffe <mcm35(a)cam.ac.uk> > Date: March 4, 2019 at 1:15:06 AM PST > To: Tom Goddard > Subject: matchmaker in ChimeraX > > Hi Tom, > > Is it possible to get the rmsd as a function of residue position when using mm in ChimeraX? I’ve turned on the verbose flag and can see the residues used to match but not their respective rmsd’s. >

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Can we draw arrows in ChimeraX?
by Steve Chou 28 Feb '19

28 Feb '19

Dear ChimeraX team, I need to draw straight and curved arrows to show the straight and twisting forces on the molecules. See the attached images (cropped from ChimeraX interface) for details. Does ChimeraX have the functionality to do this? Steve -- Steve Chou

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equivalent to "define"?
by Alexis Rohou 28 Feb '19

28 Feb '19

Hi there, Having looked through the docs a few times, I'm pretty sure I know the answer, but here goes... Is there a ChimeraX equivalent to define <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> in Chimera 1? Or any other facility to draw geometric shapes (I'm particularly interested in calculating and drawing planes)? Cheers, Alexis

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Re: [chimerax-users] Color palettes for planes and solid data?
by Tom Goddard 28 Feb '19

28 Feb '19

Hi Oli, The single plane you are showing is the “solid” style, no different from if multiple planes are shown. You can use brightness value 1 for each color if you want, but it needs to be specified, it does not default to 1 (that usually is not what people want when using solid style rendering of more than 1 plane since it would be totally opaque). Also normally single planes are shown as partially transparent in both Chimera 1 and ChimeraX. Tom > On Feb 28, 2019, at 12:34 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > I’m also unclear why for an opaque plane it is necessary to set a brightness for each map value - surely a color palette with simple color,value pairs would be fine if there is no transparency issue as there is with a 3D solid representation? > > Oli > >> On Feb 28, 2019, at 3:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Oli, >> >> To set the colors of different map values use the volume command >> >> volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green >> >> This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel. >> >> When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok. >> >> Tom >> >> >>> On Feb 28, 2019, at 11:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> Hi, >>> >>> Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! >>> >>> I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. >>> >>> Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). >>> >>> Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). >>> >>> Cheers >>> Oli >>> >>> <Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

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Re: [chimerax-users] Color palettes for planes and solid data?
by Tom Goddard 28 Feb '19

28 Feb '19

Hi Oli, There is no capability to automatically use a palette and min/max range of map values that sets the levels and colors. That might be useful although when I have done this by hand I think equally spaced colors rarely produces what I want. The cryosparc image you attached is a good example of the color spacing not producing a very informative view. At any rate, if you want this feature in ChimeraX use the Help / Report a Bug… menu entry which is also for requesting features. I just tried setting the map threshold below the lowest value in the map and clipping in Chimera 1 and it only clips a cube for me. So I’m not sure what you mean when you say that works in Chimera 1. The streaks when you color the clipped and capped surface are because the cap is composed of triangles and only the vertices of the triangles are colored and the triangles are very long and skinny. Read about the Surface Capping mesh subdivision option in Chimera 1 if you want more explanation of it. ChimeraX does not yet support the cap subdivision, but if you follow my previous suggestion it is an alternative method that can work. Tom > On Feb 28, 2019, at 12:31 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Hi Tom, > > Yes I know it is possible to do manually, thank you, but it requires quite a lot of futzing about with brightness/color pairs to get nice looking results. I was wondering if it would be possible to add support for palettes, with color thresholds automatically distributed between a minimum and a maximum, so that one can for example color a map slice with a rainbow palette between a minimum and a maximum density value (e.g. as per the density slices from cryosparc that I attached to the previous email). > > Re the cube, I set the threshold to -10 so that when I clip the map, it exposes a face that I can color by density value. I do this in Chimera and it works as expected without altering anything, here I just see streaks. I’m still unclear why I just see streaks on the clipped face no matter the threshold - this doesn’t seem to be the intended behavior? > > Oli > >> On Feb 28, 2019, at 3:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Oli, >> >> To set the colors of different map values use the volume command >> >> volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green >> >> This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel. >> >> When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok. >> >> Tom >> >> >>> On Feb 28, 2019, at 11:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> Hi, >>> >>> Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! >>> >>> I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. >>> >>> Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). >>> >>> Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). >>> >>> Cheers >>> Oli >>> >>> <Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

1 0

Color palettes for planes and solid data?
by Oliver Clarke 28 Feb '19

28 Feb '19

Hi, Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). Cheers Oli

1 0

Missing features in ChimeraX
by Tom Goddard 26 Feb '19

26 Feb '19

Hi Junha, Glad to hear you are trying VR with ChimeraX. Per-model clipping in ChimeraX is done with the clip command, or with the clipping mouse modes, atom radii are set with the size command, visibility is set with the show/hide commands, color is set with the color command, there are volume tracer mouse modes, and saving marker files should work, although you hit some bug and should press the Report a Bug… button when you get that traceback. ChimeraX does not have the selection inspector window yet. ChimeraX uses a different window toolkit Qt while Chimera used Tk so it requires all new code to move any graphical user interface from Chimera to ChimeraX. ChimeraX is a completely new program, modernizing every component of the 20-year-old design of Chimera so even moving commands from Chimera to ChimeraX requires substantial work. If you don’t find ChimeraX ready for your use, of course you should continue to use Chimera. We expect ChimeraX to replace Chimera in a few years. You might want to spend an hour skimming Elaine’s thorough ChimeraX documentation to understand what is in ChimeraX, including many new features like virtual reality that are not in Chimera. Tom > On Feb 26, 2019, at 2:03 AM, Jun Ha Song wrote: > > Tom, > > I recently got HTC Vive, and therefore started using ChimeraX. I have to say; the VR functionality is amazing. The ability to VR alone is sufficient reason for me to move over to ChimeraX. > > However, I noticed that key, crucial, irreplaceable features are (as far as I am aware) non-existent on ChimeraX. Below are function/tools that exist in Chimera that I use (literally) everyday, and I am wondering if these function/tools can also be implemented on ChimeraX or not. > > - per-model clipping (mclip) > - inspect selection (ability to change atom/bond/surface radius, visibility, color) > - volume tracer (ability to save markerset or atom/bond as .cmm) > > If the circumstance is so that implementing these onto ChimeraX is not feasible, then I must remain with Chimera until similar tools become available on ChimeraX. > > Also, is there any particular reason why all the tools of Chimera are not copied onto ChimeraX? Is ChimeraX trying to be another program that is different from Chimera? > > > > As for "ability to save .cmm", I tried saving atom/link using command > > save E:\LBNL\Stereocilia\ChimeraX_Markerset.cmm format markers models #1 > > but I got error saying that > > NotImplementedError: Slices are not implemented. > File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\markers\cmmfiles.py", line 39, in markerset_as_xml > rgb = tuple(r/255 for r in m.color[:3]) > See log for complete Python traceback. > > is this a simple bug during development, or have I typed wrong command? > > Best, > Junha Song.

1 0

How to zoom into a spot that is not located in the center gradually and straightly?
by Steve Chou 24 Feb '19

24 Feb '19

Dear ChimeraX team, Thanks for your fast and detailed responses to my questions! If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve -- Steve Chou

2 7

Can we change the lighting gradually in ChimeraX?
by Steve Chou 20 Feb '19

20 Feb '19

Dear ChimeraX team, Is it possible to change the lighting gradually in ChimeraX, e.g., from "soft lighting" to "lighting simple"? This sounds weird, but makes sense if we want to change the lighting method in a movie. Thanks in advance! Steve -- Steve Chou

2 1

help with chimerax wildcards
by Michael Lawrence 20 Feb '19

20 Feb '19

Hi, I am trying to use wild cards in chimerax but they appear not to work. I type the command color @N* blue and get as response Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword All I am trying to do is color all nitrogens blue. Version 0.5 (2018-02-05) running on macOS Sierra v10.12.6 what am I doing wrong? thanks Mike Lawrence

2 2

Blank lines in pseudobond files
by Tom Goddard 19 Feb '19

19 Feb '19

I made ChimeraX ignore blank lines and comment lines starting with “#” in pseudobond (.pb) files. Tom > On Feb 15, 2019, at 3:02 PM, Steve Chou wrote: > > Hi Elaine, > (1) I tried to read the pseudobonds from a file (.pb) , > ========================= > #1/A:13@NE2 #1/A:704@O > #1/A:13@NE2 #1/A:502@MG > #1/A:13@NE2 #1/A:501@PB > > #2/A:13@NE2 #2/A:704@O > #2/A:13@NE2 #2/A:502@MG > #2/A:13@NE2 #2/A:501@PB > ========================= > the program reported an error. > ============================= > ValueError: not enough values to unpack (expected 2, got 0) > File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file > aspec1, aspec2 = line.split()[:2] > See log for complete Python traceback. > ============================= > > (2) Then I tried to add distances on the ChimeraX terminal > ============================= > distance #1/A:13@NE2 #1/A:704@O > distance #1/A:13@NE2 #1/A:502@MG > distance #1/A:13@NE2 #1/A:501@PB > > distance #2/A:13@NE2 #2/A:704@O > distance #2/A:13@NE2 #2/A:502@MG > distance #2/A:13@NE2 #2/A:501@PB > ============================= > I was able to see the distance labels in the two structure. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. > Steve > > On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it. > > You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>> > <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>> > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou(a)gmail.com <mailto:stevezchou@gmail.com>> wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13@NE2 #1/A:502@MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > > Hi Steve, > > Actually I’m surprised the Mg and water were included (even if present at both ends) because I thought they had to be tethered by a bond or pseudobond (like a distance measurement) to the biopolymer chain, as described here under “Atoms in Common”: > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>> > > > > For the case where composition changes, you could add in a fake Mg ion and water to the structure that’s missing them, but you’d have to decide where to put them. Also it was my understanding that they had to be tethered to the biopolymer chain (e.g. add distance measurement, which can then be hidden), but maybe that requirement has changed, or the Mg does already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don’t care if the Mg or water move during the morph, you could just display those atoms from the original model (that was input to morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com <mailto:stevezchou@gmail.com>> wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. > > > (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> > > > > -- > Steve Chou > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

1 0

Fwd: [Chimera-users] Can ChimeraX morph between two surfaces?
by Steve Chou 16 Feb '19

16 Feb '19

Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB #2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. ============================= (2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. > You'd make a plain text file with name *.pb with lines like that and open > it. > > You don’t have to read in pseudobonds from a file, however. If not too > many, probably easier just to add distance monitors. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context> > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13@NE2 #1/A:502@MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Steve, > > Actually I’m surprised the Mg and water were included (even if present > at both ends) because I thought they had to be tethered by a bond or > pseudobond (like a distance measurement) to the biopolymer chain, as > described here under “Atoms in Common”: > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > > > > For the case where composition changes, you could add in a fake Mg ion > and water to the structure that’s missing them, but you’d have to decide > where to put them. Also it was my understanding that they had to be > tethered to the biopolymer chain (e.g. add distance measurement, which can > then be hidden), but maybe that requirement has changed, or the Mg does > already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don’t care if the Mg or water move during the morph, you could > just display those atoms from the original model (that was input to > morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by > shifting the structure), the "Mg ion" and the "water molecule" do not > follow the same path as the protein. They move but separate from the > protein. > > > (2) If the two conformations have slightly different compositions, the > "Mg ion" and the "water molecule" do not show up in the morphed pdb > ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: > http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > -- Steve Chou -- Steve Chou

2 5

ChimeraX equivalent to ribinsidecolor
by Lukas Kater 15 Feb '19

15 Feb '19

Hi, is there a way to change the color of the inside of helices? Something like "ribinsidecolor" in chimera. see an example here (second picture from top): https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles.html Thanks for any feedback! Lukas

2 1

Can ChimeraX morph between two surfaces?
by Steve Chou 14 Feb '19

14 Feb '19

Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou

2 5

bug report: hide with silhouettes
by Alexis Rohou 11 Feb '19

11 Feb '19

Hi Elaine, ChimeraX team, When silhouettes is set to true, hiding all models causes a bug whereby the display panel is not responsive / redrawn. As far as I can tell other parts of the GUI are still working. Below is a minimal reproducer. Attached are screenshots of what I'm seeing when silhouettes true (bug) or silhouettes false (no bug). I am running this on MacOS 10.13.6 on a MBP with graphics "Intel Iris Plus Graphics 650 1536MB" (sorry not sure what might be relevant here), and the Chimera version is: UCSF ChimeraX version: 0.8 date: 2018-12-17 22:26:30 UTC branch: v0.8 commit: 412d62d1949722ed7f52b3e515ec0f3b70b6b7af Python: 3.6.4 Obviously there's a workaround to avoid this but this caught me a few times in the last couple of days and it'd be nice to not have to watch out for it because the only solution I've found so far is to quit ChimeraX and start again. Cheers, Alexis PS. here's the reproducer: open pdb:1tbq set silhouettes true # Hide stuff hide #!1 models # Wait a bit (alternatively stop here and return to interactive use before doing the next step) wait 100 # print version out version verbose # Try to show it again. This should work (and does if silhouettes false) show #!1 models

3 4

volume zone - unexpected behavior when newMap false
by Alexis Rohou 11 Feb '19

11 Feb '19

Hello, I've been playing with volume zone and having good fun, but... I've noticed that if I set newMap to false, then the invert option is ignored (behavior is as though invert is false, even when I specify invert true). When newMap is set to true, or not set at all, the invert option has the effect I expected from reading the documentation. Am I missing something? Hopefully description above is unambiguous but let me know if you need step-by-step. Cheers, Alexis

3 4

Can ChimeraX add noise (Brownian-like motion) in morphing?
by Steve Chou 11 Feb '19

11 Feb '19

Dear ChimeraX support, When morphing from one structure to another unaligned structure, ChimeraX follows a smoothly curved path? Can it add noise (Brownian-like motion) to the path? All the best, Steve -- Steve Chou

2 3

equivalent to "move cofr"
by Alexis Rohou 08 Feb '19

08 Feb '19

Hello, Switching to ChimeraX, I find myself looking for an equivalent to "move cofr <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html#cofr>". Is there one? The use case is: I'm working on a particular part of a map & structure, I open a structure of a homologuous domain from the PDB, but its coordinates are way off, and I want to move it to the region I'm working on without having to zoom out and drag it. My apologies if this is in the documentation somewhere, I'm still finding my way around. Cheers, Alexis

2 2

Output motion prickle magnitude
by Scott, Brandon L. 08 Feb '19

08 Feb '19

Using the measure motion command I am able to generate the prickles on the surfaces correctly, which is great for visualization. Is it possible to write the magnitude of those prickles, and the index to a file so we can do further analysis on the distributions? Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

2 1

How to align two molecules using a subset of atoms in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX support team, I tried the following command first - it worked well. ================== match #1/A to #2/A ================== Then I tried to align the two molecules using parts of them - it didn't work and complained that "No chains in reference structure PROT.pdb #2 compatible with BLOSUM-62 similarity matrix." ================== matchmaker #1/A:10-20@CA to #2/B:10-20@CA ================== System Info: ================== Platform: Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo ChimeraX version: 0.9 (2019-02-05) ================== Thank a bunch! Steven -- Steve Chou

2 3

How to re-define the secondary structure info in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX developers and users, In Chimera, I can use the following commands to redefine the secondary structure info. ============================ setattr r isHelix false : setattr r isSheet false : setattr r isSheet true :8-12,16-21 setattr r isHelix true :55-61,78-92 ============================ What's the ChimeraX equivalent? By the way, I can also delete the hydrogen atoms using "delete element.H" in Chimera. Is there an equivalent in ChimeraX? Many thanks in advance! Steve -- Steve Chou

2 1

Bio-Formats with ChimeraX?
by Matthew Akamatsu 07 Feb '19

07 Feb '19

Hi, I just started using ChimeraX to render and save 3D time lapse microscopy data as a high-performance replacement of Fiji. I am wondering how flexible ChimeraX can be in opening different TIF-derived file formats - particularly hyperstacks (multi color, multi Z, multi time). Other desired formats would be proprietary formats like .nd2 and .sld . Bio-Formats does all of this in an open-source manner - how feasible would it be to have bio-formats type functionality in ChimeraX? Thanks, Matt

2 3

VR in ChimeraX and Dell Visor
by Lewandowski, Jozef 24 Jan '19

24 Jan '19

Hi, Has anyone tested Dell Visor for VR in ChimeraX? If yes are there any issues you have run into? I am assuming that the experience should be similar to what Tom has described for Samsung Odyssey but I would appreciate if anyone had specific feedback on this particular piece of hardware. Thanks, Józef

2 1

color by conservation
by George Ghanim 16 Jan '19

16 Jan '19

Hello, Is it possible to color amino acids by conservation from an alignment file? Thanks, George Ghanim —— PhD Student Rio Lab Molecular and Cellular Biology, University of California Berkeley

2 1

ChimeraX crashes from time to time on Lenovo Y530
by Yehuda Halfon 02 Jan '19

02 Jan '19

Hi All, I bought a new laptop, Lenovo Y530 which has GTX 1050Ti as well as the intel 8750H which has UHD 630 and 16 GB of ram with windows 10. Chimerax is installed on m.2 drive. Sometimes, without any correlation it freezes and crashes, when I restart the error in the picture. All the drivers are updated. I run chimerax with the GTX as the GPU. I think it's something with the dual GPUs, is there a fix for it? I tried both 0.7 and the new 0.8 (not daily). On my other laptop, an old Macbook pro it run perfectly. Thanks, Yehuda Halfon

3 2

Movie recording error
by Carlos Escalante 21 Dec '18

21 Dec '18

Dar all, Trying to make a morphing movie. Everytime I run it, it comes out with the following error: Unknown command: coordset #3 1,21 And there is no sign that is recording. The same error occurred when I created the morphing, but it did created the morphing. Also, if I try to change anything and run the command again, it says ‘already recording a movie’ Any suggestions? Thank you Carlos R. Escalante Assistant Professor Department of Physiology and Biophysics VCU School of Medicine 1220 East Broad Street MMRB 2040 Richmond VA 23298 carlos.escalante(a)vcuhealth.org 804-628-1202

2 1

version 0.7
by jingdong cheng 21 Dec '18

21 Dec '18

Hello, Could you provide me the older version 0.7? I tried the new 0.8, it is good, fixed a lot of bugs, but it runs super slow slow. It is better to change back to 0.7, but on your website I can’t find it anymore. Cheers! Merry Christmas! Jingdong

2 1

FW: hi
by Williams, Joanne 21 Dec '18

21 Dec '18

From: mosbah amine <aminemosbah(a)hotmail.com> Date: Thursday, December 20, 2018 at 11:24 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: hi dear colleague trying to download chimiraX , no way to get to the right page !!! would you please send me the zip file , i agrre to licesing requarements also i have a windows10 for compatibility regards Dr mosbah amine TN

2 1

scale bar in chimerax
by Xu Jingwei 13 Dec '18

13 Dec '18

Hi, I recently installed the ChimeraX in my centos 7 and it is really powerful software to make beautiful figures. I really like it! However, one question before I setup for figures is how could I make a scale bar in ChimeraX? I did not find the relative information in the web. Could you please help me about that? I am really appreciated for that. Best, Jingwei ETH Zürich Dr. Jingwei Xu Postdoc Institute of Molecular Biology & Biophysics Department of Biology HPK D17 Otto-Stern-Weg 5 8093 Zürich, Switzerland

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Dual GPU VR support
by Lewandowski, Jozef 11 Dec '18

11 Dec '18

Hi, A quick question. Does implementation of VR in ChimeraX support dual GPU? Or dual GPU would give no advantage? Thanks, Józef

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transparentBackground doesn't seems to work on save
by Yehuda Halfon 09 Dec '18

09 Dec '18

Hi all, We are trying to save an image without a background using save image filename format png transparentBackground true but we get the error: transparentBackground expected key word. What are we doing wrong? Thanks, Yehuda Halfon

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Incrementing value in perframe
by Scott, Brandon L. 09 Nov '18

09 Nov '18

I am attempting to use the measure convexity on each frame, and seem to have a mismatch between the frame number which goes from [0 - (N-1)] and the volume child which goes from [1 - N]. Is there a way to augment the $1 value to be $1+1? Attached are the command calls. This displays the convexity properly on the called frame: vseries play #1 jumpTo 1; measure convexity #1.2 smoothingIterations 12 palette cyan-gray-maroon range -1,1; The does not display it because of the mismatch: movie record; perframe "vseries play #1 jumpTo $1; measure convexity #1.$1 smoothingIterations 12 palette cyan-gray-maroon range -1,1;" range 1,200; wait 200; movie encode C:\Users\LLSM\Desktop\Convexity.mp4 quality highest framerate 25 Thanks in advance. -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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Render images in nogui mode
by Lukas Pravda 07 Nov '18

07 Nov '18

Hi all, I was wondering if there is a way how to generate images from linux terminal. I’ve come across a couple of very old posts in the mailing list stating that this was not possible at that time. So, I wonder if anything has changed. If I use cif files only, chimerax gives “Unable to render images to save them” message. If I try to include volumetric data from cryo-EM overlaid on the structure I get an exception during opening a *.map file. Please see the script below. The exception is in the attachment Best, Lukas open emd_8909.map volume #1 color white transparency 0.7 level 0.1 step 1 zoom 1.2 open 6ds5.cif set bgColor white hide selAtoms show selAtoms ribbons color bychain ribbons light full light shadow true save image default.png width 1600 height 1600 supersample 5 transparentBackground true turn y 90 save image y.png width 1600 height 1600 supersample 5 transparentBackground true turn z 90 save image z.png width 1600 height 1600 supersample 5 transparentBackground true

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chimeraX questions on representation
by Dr. Eddie 16 Oct '18

16 Oct '18

Hi, I have a few small n00b questions that would really help me along. 1) How do I change the "ball scale" property in chimeraX using a command for the sphere representation? 2) When I do "select protein" (which is represented as a cartoon) it highlights it but clicking on any of the buttons to change the representation does nothing. I need to click first on the show atoms and then I can click on those but many of the H are not connected (for LYS I have two white dots floating above the carbon with no bond to them, but a bond to other C's and it is only for one CH3 group, the other is fine). This is true in all three representations. How do I fix this? 3) Can I increase the resolution in VR? 4) After clocking on the label tool with a VIVE controller and using it, how to I change it back to the original mode so I can scale the model (using both triggers)? Thank you very much for your help! Eddie

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Re: [chimerax-users] chimeraX questions on representation
by Eric Pettersen 16 Oct '18

16 Oct '18

Hi Eddie, ChimeraX (and Chimera for that matter) connect atoms in standard residues using a connectivity template. Therefore the atoms have to have standard names. Some hydrogens in your file don’t have their PDB-standard names, and therefore wind up unconnected. I have committed a fix for this — if there are unconnected hydrogens after the template pass then Chimera(X) does an additional connect-by-distance pass. A second problem with the file is that it uses ATOM records for everything, including solvent, ions, and the lipid bilayer. ATOM records are for polymeric residues and imply connectivity between consecutive residues with the same chain ID. Therefore the non polymeric components of the file should have been using HETATM records. I have attached an edited version of your file with appropriate HETATM records. It should work much better in tomorrow’s fixed build. —Eric > On Oct 16, 2018, at 11:31 AM, Dr. Eddie <eackad(a)gmail.com> wrote: > > Thanks for the help! As for the pdb, I've attached it. It shows fine in vmd and pymol. > Thanks, > Eddie > > On Tue, Oct 16, 2018 at 1:19 PM Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> On Oct 15, 2018, at 8:35 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> I don’t know why your H’s are disconnected specifically, but it’s almost surely some issue with the input file. > > If you provided the input file, we might be able to offer advice on how to get ChimeraX to handle it better. One thing you might try sight unseen is to remove the LINK/CONECT records in the file (assuming it’s a PDB file). > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > > > > -- > Eddie > <popc.3a4.ionf.pdb>

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Question about measuring the distance of helix axis
by ze li 16 Oct '18

16 Oct '18

Dear ChimeraX supporting team: I try to measure the distance between two helix axises, but in the "distance" command there is only atom-to-atom usage in Chimera X. Is there any command and plugin for this function, such as in Chimera? Thank you. Best,

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symmetric function from different template in chimera x
by Alexei Hernandez 09 Oct '18

09 Oct '18

Good morning, I am currently utilizing chimera x for different modeling features. Right now I am trying to use the symmetric option for a file created by a peer of mine titled ppar.pdb. I added the file here and trying to use the sym function by using the template of a close protein blast result, one called 3DZU, also added it. I want to use the template of the 3dzu to create a structure for ppar. I am confused as to which command line to use out of all of them and if it is possible to use 3dzu as a template for the ppar file created. Could you please help me with the command line. Have a nice day... Alexei Hernandez

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Re: [chimerax-users] [Chimera-users] FW: Contributing to ChimeraX ?
by Tom Goddard 01 Oct '18

01 Oct '18

Hi Nicholas, The ChimeraX OBJ reader is all in Python with source code included in the distribution. Windows chimerax/bin/lib/site-packages/chimerax/wavefront_obj Linux chimerax/lib/python3.6/site-packages/chimerax/wavefront_obj Mac ChimeraX.app/Contents/lib/python3.6/site-packages/chimerax/wavefront_obj The ChimeraX git repository is here https://www.rbvi.ucsf.edu/trac/ChimeraX/browser <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser> I don’t think the repository can be cloned due to access restrictions, but here is some info about that and you can try and see if it works. https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html Tom > On Oct 1, 2018, at 7:52 AM, Williams, Joanne wrote: > > > > From: Nicholas Yue > Date: Sunday, September 30, 2018 at 3:40 AM > To: "chimerax(a)cgl.ucsf.edu <mailto:chimerax@cgl.ucsf.edu>" <chimerax(a)cgl.ucsf.edu <mailto:chimerax@cgl.ucsf.edu>> > Subject: Contributing to ChimeraX ? > > Hi, > > I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly. > > I was hoping I can take a look at the source code to attempt to fix it myself. > > I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to? > > If I need to sign any documents before contributing, let me know :-) > > I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc. > > Cheers > -- > Nicholas Yue > Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5 > Custom Dev - C++ porting, OSX, Linux, Windows > http://au.linkedin.com/in/nicholasyue <http://au.linkedin.com/in/nicholasyue> > https://vimeo.com/channels/naiadtools <https://vimeo.com/channels/naiadtools>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Re: [chimerax-users] [Chimera-users] chimerax mesh commands doesn't work
by Elaine Meng 20 Sep '18

20 Sep '18

Hi Yehuda, I don’t think you are doing anything wrong; in ChimeraX, the lineThickness option doesn’t work for me either, although it works fine in Chimera on the same computer — we will look into it. Sorry for the inconvenience and thanks for reporting, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there is a chimerax-users(a)cgl.ucsf.edu mailing list too <http://rbvi.ucsf.edu/chimerax/docs/contact.html> > On Sep 20, 2018, at 4:56 AM, Yehuda Halfon <yehuda.halfon(a)weizmann.ac.il> wrote: > > Hi all, > I wanted to use chimeraX to use some commands on mesh display. > Some works like meshLightning but others like lineThickness doesn't > I use volume #1 lineThickness 10 (or any other integer) but nothing seems to change. What am I doing wrong? > Yehuda Halfon

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Ca trace
by v.kalienkova＠bioc.uzh.ch 19 Sep '18

19 Sep '18

Dear all, I was wondering, is there an option to just show a Ca trace in ChimeraX? If yes, can one modify the width of it? Thanks a lot in advance, Valeria

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Forward of moderated message
by chimera-users-bounces＠cgl.ucsf.edu 17 Sep '18

17 Sep '18

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ChimeraX - Color by Electrostatic Potential
by Maurício Menegatti Rigo 14 Sep '18

14 Sep '18

Hi, is there a way to color the protein surface according to Electrostatic Potential, just like we do with Chimera ("Electrostatic Surface coloring" under "Tools"). The input potential file was calculated with Delphi. Thanks in advance, Maurício Menegatti Rigo, *Ph.D.* Brazil

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Saving obj file
by Donghyun Park 13 Sep '18

13 Sep '18

Dear ChimeraX-users, I have a question about saving the scene as obj file. In the traditional Chimera, I was able to generate obj file with texture by simply clicking 'save' button. I tried to save obj file simply by typing *save ~/Desktop/file.obj . *I generated obj file but it does not show texture - basically black &white. I was hoping to find some more information on the user guide but I did not find much. Could somebody please help me with this problem? Thank you, Raphael

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Thank you for your free vector icons.
by Moira Ames 11 Sep '18

11 Sep '18

Hi, I hope this email finds you well. Thank you for making this page: https://www.cgl.ucsf.edu/chimerax/docs/embedded.html I recently passed my thesis with a lot of aid from that resource page. It has helped us tremendously. May I ask if you are still updating the page? If you are, I would like to repay you by way of recommending an additional resource which could be a good addition to it. Here it is: https://www.webhostingsecretrevealed.net/free-icons/. <https://www.webhostingsecretrevealed.net/free-icons/> I hope you find it useful and helpful as well. Best Regards, Moira Ames *Graduating student from University of St. Thomas*

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Apply dust command to entire timeseries
by Scott, Brandon L. 10 Sep '18

10 Sep '18

I am attempting to remove small connected components from my timeseries volumes. The surface dust command works well for this, but it only works on one time point at a time, is there a way to script this, or use in conjunction with the vseries play command to apply this to each timepoint? Thanks, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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Re: [chimerax-users] invert selection in ChimeraX
by Yashar Sadian 10 Sep '18

10 Sep '18

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Re: [chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization
by Tom Goddard 04 Sep '18

04 Sep '18

Hi Pascal, I enhanced the ChimeraX select command so you can select the crosslinks in a length range. Then you can color the selected ones. For example, select #1.1 minimumLength 30 color sel red select #1.1 minimumLength 5 maximumLength 10 color sel yellow sel #1.1 min 10 max 15 color sel blue The minimumLength and maximumLength options will be in tonight’s ChimeraX builds (available around 5 AM Pacific time). Tom > On Sep 1, 2018, at 2:57 AM, Pascal Albanese wrote: > > Dear Support Staff, > > first of all many thanks for developing Chimera! > > I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): > > - Is it possible to load different sets of distances/crosslinks (like with different IDs)? > - is it possible to color code the distances with a cutoff (like red if >30 for instance)? > - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) > > that's it, maybe something can be done writing the code but unfortunately it's not my job. > > Thanks a lot and looking forward to hear from you, > > Cheers, > Pascal > > -- > Pascal Albanese, PhD > Post-doc, Politecnico di Torino > Dipartimento DISAT, > BioSolar Lab@Environment Park > > Via Livorno 60 > > 10144 Torino > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization
by Elaine Meng 04 Sep '18

04 Sep '18

Hi Pascal, Many features are are still in development, so although we can easily imagine useful features (and we welcome your suggestions), many are not yet implemented. Yes, you can load different sets of crosslinks. The “pseudobond” input format is just plain text specifiying pairs of atoms. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic> Then you can specify the different models (input file -> model) in the “crosslinks histogram” command by their numbers as shown in the Models panel, e.g. crosslinks hist #1.3 crosslinks hist #3 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram> Currently there isn’t color-by-length or selection-by-length, sorry. The interaction with the histogram that you may already have seen is that passing the cursor over the columns of the histogram temporarily enlarges the corresponding-length pseudobonds and hides the others. There isn’t control over how wide the histogram bars are. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there’s a chimerax-users mailing list CC’d on this message which you can send to and/or join > On Sep 1, 2018, at 2:57 AM, Pascal Albanese <pascal.albanese(a)polito.it> wrote: > > Dear Support Staff, > > first of all many thanks for developing Chimera! > > I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): > > - Is it possible to load different sets of distances/crosslinks (like with different IDs)? > - is it possible to color code the distances with a cutoff (like red if >30 for instance)? > - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) > > that's it, maybe something can be done writing the code but unfortunately it's not my job. > > Thanks a lot and looking forward to hear from you, > > Cheers, > Pascal

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FYI: Model.id_string API change
by Eric Pettersen 22 Aug '18

22 Aug '18

For those of you writing code in ChimeraX, in case you’re using Model.id_string you should know that as of tomorrow’s build, Model.id_string is a property instead of a function. —Eric Eric Pettersen UCSF Computer Graphics Lab

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question about chimerax
by Fang, Fei 14 Aug '18

14 Aug '18

Hi, This is Fei from University of Pittsburgh. Here is a question about chimera x. By introducing two structures into the chimera x, how can I move the one structure over so that they're no longer covering each other? Thanks. Best, Fei

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Export a scene from Chimera and into ChimeraX?
by Oliver Clarke 06 Aug '18

06 Aug '18

Hi, I love the new visualization features in ChimeraX, but I also really like the depth of functionality available in the original Chimera. I understand that ChimeraX has been rebuilt from the ground up and therefore can’t be expected to support importing sessions from Chimera1. However, Chimera1 is also able to export static scenes - e.g. as COLLADA or VTK format. Would it be possible to add an import function for these scenes in ChimeraX, so we can create a static scene just the way we like it in Chimera1, and then render it with e.g. ambient occlusion etc in ChimeraX? Alternatively/additionally, would it be possible to add an export function for molecular surfaces to ChimeraX? One of the major improvements in ChimeraX (at least for my work) is that it has a robust and fast surface calculation function that works on large, multi chain structures. Would it be possible to export these surfaces (e.g as MRC format) so they could be imported into Chimera1? Cheers Oli

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Setting the bgColor transparent in ChimeraX
by bertrand beckert 03 Aug '18

03 Aug '18

Dear all, I have now been trying to use ChimeraX as a replacement for Chimera for making really nice images for publication. So far I have to say I really liked the rendering! definitely a really nice work! However I was really wondering how to get the background transparent... In Chimera we were able to set the background transparent as preference which is actually really useful... any idea how we can to do it in ChimeraX? Any help would be highly appreciated! Best Bertrand

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Transparency and Scaling factor in ChimeraX
by Christoph Bachmann 31 Jul '18

31 Jul '18

Dear ChimeraX team First of all, great piece of software. It's a lot more userfriendly than pyMol or VMD. But it is hard to find information, since most is still for the old Chimera. I'm struggeling to get transparency in saved pngs to work. I've tried it on a PC and a Mac with no luck. This is strange since both computers support transparency and I regularly work with that feature so it can't be a hardware problem. My main question is how to get absolute sizes of the molecules. I'm currently making an illustration with different molecules, from small to large and I want their size to be displayed as accurate as possible (so a carbon atom in one molecule is exactly as big as the one in another molecule). I'm sure there is an easy way but I haven't found anything so far. If I would load them all into ChimeraX their sizes are represented correctly, but that's just too much for the computer. So, thanks in advance for your help. Best wishes Christoph Bachmann University Basel - Switzerland

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How to not build bundles/use wheel?
by Yuri 25 Jul '18

25 Jul '18

I am trying to build on FreeBSD. It calls the module 'bundle_builder', which calls 'wheel'. How to only do a regular python build, and not call 'wheel'? Thanks, Yuri

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Volume isosurface transparency
by Zack Gainsforth 24 Jul '18

24 Jul '18

Hi, I’m fairly new to ChimeraX so forgive me if I’m a bit ignorant in this question. I have volumes acquired by tomographic reconstruction of STEM/EDS data (elemental composition in an electron microscope). I want to visualize several elements together as different colors representing phases. In some cases, the boundary is fairly obvious and can be represented with an isosurface. When I try to set the transparency of the isosurface so I can see the objects inside it, it simply turns darker color rather than transparent. As an example, here is a silicon isosurface obscuring the other volumes inside it: I’m setting the transparency using the colors dialog box: For comparison, if I make the isosurface invisible to show the objects inside: If instead I use the transparency command: volume #5 transparency 50 The isosurface turns black: My question is: am I doing this incorrectly? Thanks, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 zackg(a)ssl.berkeley.edu

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Re: [chimerax-users] I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by Eric Pettersen 20 Jul '18

20 Jul '18

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

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Hardware for VR of volume data
by Tom Goddard 11 Jul '18

11 Jul '18

Hi Bernard, VR is not going to handle large volumes no matter what hardware you buy. To avoid causing nausea current VR headsets use 90 frames/second graphics updating. That is in two eyes, so the effective graphics frame rate needed is 180 frames/second. By comparison on a flat panel display it is routine to show a very large volume at 10 frames per second and this causes no problem. So VR requires about 20 times the rendering speed of visualization on a conventional display. So here are some ideas of what you can expect. Some recent 3d light microscopy I was looking at in VR is 4K by 2K by 31 z planes with 3 channels — and it rendered fast enough with VR on a GTX 1080 and also on a Quadro P6000. Comparing to your 2K cubed example my data was equivalent to about 2k x 2k x 186, or about 1/10th the size. I haven’t benchmarked volume rendering so I don’t actually know at what size graphics is too slow — I should test this. But I suspect this is close to the limit. For molecular structure display, 100,000 atoms with very coarsely triangulated spheres works in VR but is near the limit. For surface and triangle rendering the limit is about 2-5 million triangles depending on which high-end graphics card before frame drops start causing flicker. For molecules showing 2.4 million atoms of HIV capsid 3j3q is fine on a desktop display but is not going to work in VR. With that in mind I would recommend a GTX 1080 Ti graphics card with a high-end CPU, maybe 64 Gbytes of memory, definitely get a high-end SSD drive or two as the data transfer rates of about 3 Gbytes/second are very handy for large data compared to the 100 Mbytes/second of spinning drives — the whole system would be about $4-5k. You could spend more but you won’t get any better performance. The main VR performance bottleneck is going to be in the software if you use ChimeraX. Unfortunately it does color blending and mapping data values to colors and cropping on the CPU instead of the GPU which is painfully slow, tens of seconds to adjust brightness on the above-mentioned 3-channel light microscopy. I expect to put the blending and color lookup on the GPU in ChimeraX over the next 12 months. Tom > On Jul 10, 2018, at 12:48 PM, Heymann, Bernard (NIH/NIAMS) [E] wrote: > > Hi > > I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? > > Bernard > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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pdb and map colors
by Andrey Feklistov 25 Jun '18

25 Jun '18

My question is about ChimeraX 0.6: is it possible to highlight different parts of a pdb (based on the protein sequence) with different colors and then color a corresponding map accordingly. I can't find an option 'Sequence' like in the old Chimera, is it possible to do this from a command line? Thanks!

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Re: [chimerax-users] [Chimera-users] ChimeraX won't start on Ubuntu 16.04
by Greg Couch 22 Jun '18

22 Jun '18

(This is really a question for the chimerax-users mailing list, not the chimera-users one.) If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04). But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem. Regards, Greg On 06/21/2018 10:34 AM, Petr Leiman wrote: > Dear ChimeraX users and Developers, > > ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 > machines. The error message is as follows: > > This application failed to start because it could not find or load the > Qt platform plugin "xcb" > in "". > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, > offscreen, vnc, xcb. > > Reinstalling the application may fix this problem. > Fatal Python error: Aborted > > Current thread 0x000014f406ce7740 (most recent call first): > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", > line 93 in __init__ > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 485 in init > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 788 in <module> > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 85 in _run_code > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 193 in _run_module_as_main > Aborted (core dumped) > > A few more errors while checking for missing libraries (ldd) of > ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so > or libqxcb-egl-integration.so > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version > `Qt_5_PRIVATE_API' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 > > Do I need to do a system-wide replacement of Qt5 for a different > flavor (OpenGLES)? > > Thanks, > > Petr > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

3 3

Questions about ChimeraX and problems re-downloading Chimera
by Steven Douglas Aird 21 Jun '18

21 Jun '18

Dear Elaine, Is there a way in ChimeraX to specify colors for individual species of amino acids? I would like to color cysteine residues to illustrate disulfide bonds. There appears to be no ‘byresidue' or ‘byaminoacid’ command. Since I had formerly done this in Chimera, I sought to re-download that from: https://www.cgl.ucsf.edu/chimera/download.html This page has been unresponsive for hours and the download cannot be completed. Thanks for your help, as always. Sincerely yours, Steve Aird Steven D. Aird Technical Editor Faculty Affairs Office Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

2 1

Color clip plane
by Reza Khayat 15 Jun '18

15 Jun '18

Hi, I'm coloring a cryo-EM image reconstruction based on its local resolution. Thus, the image reconstruction will contain multiple colors. Is it possible to color the clipping plane the same as the underlying image reconstruction? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

2 1

Deactivate model
by Reza Khayat 12 Jun '18

12 Jun '18

?Hi, Is it possible to deactivate a model like in Chimera? I wan to manually align a cryo-EM image reconstruction to another before using the fit command. The orientations are too different for fit to work. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

2 2

naming chain ids
by Andrew Macrae 06 Jun '18

06 Jun '18

To whom it concerns I am wondering if it is possible to change the names of the models in chimera X in a similar manner that was possible in chimera. When I split a large complex such as the ribosome it is nice to rename them so I don't need to memorize or reference the PDB what all the numbers and or letters mean. Thanks Cheers, Andrew MacRae

2 1

can now bundle user documentation with ChimeraX bundles
by Greg Couch 30 May '18

30 May '18

Starting with the next daily build, it is possible to have documentation for the tools and commands in the bundle automatically integrated into the User's Manual index. In the bundle_info.xml file, add the documentation to the DataFiles section, e.g.: <DataFiles> <DataFile>docs/user/commands/tutorial.html</DataFile> <DataFile>docs/user/tools/Tutorial_GUI.html</DataFile> </DataFiles> As you can see above, the documentation is in a directory hierarchy that matches the hierarchy of the builtin documentation. The file name for the tool should be the tool's name with underscore's replacing any spaces followed by .html. The file name for commands should be the the first word in the command name followed by .html. If help is asked for a subcommand, then a named reference is made to the subcommand, i.e., /command/.html#/subcommand/. -- Greg

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Re: [chimerax-users] Question about Space navigator and ChimeraX
by Tom Goddard 29 May '18

29 May '18

Hi Rod, I just tried SpaceNavigator with the May 29, 2018 ChimeraX build on macOS 10.13.4 and it worked. Are you still getting the error that it cannot load _spacenavigator? Are you trying to use it on Mac or Windows or Linux? And does space navigator work with Chimera on that same machine? Tom > On May 29, 2018, at 12:17 PM, Tweten, Rodney K. (HSC) wrote: > > Hi Tom, > I downloaded the latest ChimeraX daily build (2018-05-29 02:45:16 PDT), but the space navigator still does not appear not work. Was it included in this build? Thanks! > > From: Tom Goddard <goddard(a)sonic.net> > Date: Friday, May 25, 2018 at 4:33 PM > To: "Tweten, Rodney K. (HSC)" <Rodney-Tweten(a)ouhsc.edu> > Cc: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > Subject: [EXTERNAL] Re: [chimerax-users] Question about Space navigator and ChimeraX > > Hi Rod, > > Our Mac ChimeraX build machine did not have the Space Navigator library installed so it did not compile the module to use Space Navigator with ChimeraX. I've installed it on the build machine so hopefully tonight's build will have Space Navigator support. It works on my development machine. Thanks for reporting the problem. > > Tom > > > >> On May 25, 2018, at 11:02 AM, Tweten, Rodney K. (HSC) wrote: >> >> I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! >> >> <image001.png> >> >> Cheers, >> Rod Tweten, Ph.D. >> George Lynn Cross Professor >> "It's a great life if you don't weaken" >> >> Microbiology & Immunology >> BMSB-1053 >> 940 Stanton L. Young Blvd. >> The University of Oklahoma Health Sciences Center >> Oklahoma City OK 73104 >> USA >> >> >> _______________________________________________ >> 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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…>

1 0

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

25 May '18

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

2 1

info selection
by Wei Wang 14 May '18

14 May '18

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

3 2

setattr m stickScale
by Wei Wang 14 May '18

14 May '18

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

2 1

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

03 May '18

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

2 1

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

02 May '18

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

1 0

mutitouch mac
by Edoardo Gianni 01 May '18

01 May '18

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

3 3

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

01 May '18

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

2 1

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

17 Apr '18

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

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

10 Apr '18

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

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

02 Apr '18

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

1 1

morph and surfaces
by Giorgio Luciano 02 Apr '18

02 Apr '18

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

2 2

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

29 Mar '18

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

3 2

Export as .obj
by Boris Chaumette 28 Mar '18

28 Mar '18

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

2 1

Matrixset equivalent
by Reza Khayat 15 Mar '18

15 Mar '18

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

2 1

VR mode not working
by Sebastian Poelsterl 13 Mar '18

13 Mar '18

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

2 3

Some core modules moving
by Eric Pettersen 07 Mar '18

07 Mar '18

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

1 0

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

06 Mar '18

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

3 4

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

23 Feb '18

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

2 1

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

19 Feb '18

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

2 1

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

15 Feb '18

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

3 9

ChimeraX surface coloring
by Nadishka Jayawardena 14 Feb '18

14 Feb '18

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

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spin movie error
by Andrey Feklistov 05 Feb '18

05 Feb '18

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

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2dimage?
by Emmott, Ed 31 Jan '18

31 Jan '18

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

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

31 Jan '18

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

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

30 Jan '18

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

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Cannot load Chimera X session
by Donghyun Park 29 Jan '18

29 Jan '18

Dear Chimera X users, I have trouble opening saved session in Chimera X. It loads my session for few seconds that shows following error messages: KeyError: 12 File "/private/var/folders/z_/sd6vflps0hs03gjrv5gt73yw0000gr/T/AppTranslocation/A86A6FCF-9B92-4C93-98CE-D4ADBB890140/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/tools.py", line 333, in remove del self._tool_instances[tid] See log for Python traceback. Can anyone please help me? Thanks, Raphael Park

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Question regarding making movies & changing voxel size
by Donghyun Park 18 Jan '18

18 Jan '18

Dear Chimera X community, Currently, I am in a transition from the old Chimera to Chimera X. So far, I am very much enjoying Chimera X. 1) I was wondering if there's Chimera X equivalent of 'savepos' and 'movie recorder' . 2) Also, how can I change the voxel size in Chimera X? I tried to find answers in the User Guide but I couldn't find the right answer. I hope I can get some advice here. Thank you! Best, Raphael Park

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making color zone transparenct
by Yashar Sadian 05 Jan '18

05 Jan '18

Dear all Is there a command or a way to make a zone colored EM map transparent? -- Best, Yashar Sadian Christoph Mueller's group Structural and computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg, Germany Phone: 0049-6221-387-8496 Email: sadian(a)embl.de

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invert selection in ChimeraX
by Yashar Sadian 26 Dec '17

26 Dec '17

Hi is there a command to invert selection like in chimera? or simply hide whatever that is not selected -- Best, Yashar Sadian Christoph Mueller's group Structural and computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg, Germany Phone: 0049-6221-387-8496 Email: sadian(a)embl.de

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windows compatibility
by Sandrine Le Goff 19 Dec '17

19 Dec '17

Hi I would like to know if ChimeraX can be downloaded on a computer using windows 7 operating system Thanks a lot Best regards Sandrine Le Goff -- ___________________________________________ Sandrine VADON - LE GOFF Equipe Moali - Métalloprotéases et remodelage tissulaire Institut de Biologie et Chimie des Protéines UMR 5305 - Biologie Tissulaire et Ingénierie Thérapeutique - CNRS/Université de Lyon 7, passage du Vercors 69 367 LYON Cedex 07 FRANCE tel : 33(0)437652928

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Export formats
by Mike Goodstadt 11 Dec '17

11 Dec '17

Hi Tom, What formats are you planning to support for exporting scenes? Many thanks, Mike Goodstadt mikegoodstadt(a)gmail.com skype: mikegoodstadt +34 653 756 614

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Mapping local correlation between two maps
by Reza Khayat 06 Dec '17

06 Dec '17

Hi, Chimera allows one to map the CC between two maps onto a map and color the surface using the following commands: vop localCorrelation #0 #1 scolor #0 volume #2 cmap 0.6,red:0.7,white:1,blue I'm having difficulty executing the second command -mapping the values onto the first volume and assigning colors. Any help would be appreciated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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activate model selectively
by Gabor PAPAI 29 Nov '17

29 Nov '17

Dear ChimeraX developers, I have a very naive question: how can I activate models selectively, like in Chimera? I would like to superimpose a density map with a pdb, but I don’t find how I can only activate and move the pdb. Thank you in advance for your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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VR and optional functions
by Matthias Wolf 26 Oct '17

26 Oct '17

Hi Tom et al, Great job on chimeraX! The rendering engine is incredible. I have tried to view our cryo-EM volumes in VR with a new HTC Vive – it’s amazing and it works really well! ChimeraX supporting VR was one of the reasons for me to buy the Vive. Thank you! Now I haven’t used chimeraX before (I have used chimera since many years). I understand that the program is still work in progress. However, I am really missing some of the nice functions of chimera that make it so useful with a “clicky” interface - e.g. color surface by radius or by pdb properties, segmented isocontoured maps, clipping planes, subvolumes, combined shaded and wireframe surfaces, biological assembly, etc – I find these functions very useful and there don’t seem to exist any command line options for this, or I just haven’t studied them enough yet. Many of the existing menus in chimeraX have a fraction of the functionality of their sister program chimera. E.g. volume viewer, model panel, side view – I still have not figured out how to activate only one of several objects for rotation, when in chimera a click on the activate check box in the model panel does that (there is no active checkbox in the model panel of chimeraX and I couldn’t find a command to activate an object). It would be nice if one could simply grab an object in VR and rotate by itself it instead of the entire scene. Do you have a plan to add or port some of these beloved GUI functions from chimera into chimeraX? Could they be added by copying python modules from chimera? It would be great, if one could press a button in VR on the hand controller to display the menu and select functions “by virtual laser pointer”. This could preserve the development effort that went into the GUI design of chimera by reusing it in chimeraX as an identical projected 2D menu in VR and it would prevent having to take the goggles off for simple model adjustments. Best regards, Matthias

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Re: [chimerax-users] error when save sessions of chimeraX in Ubuntu
by Elaine Meng 19 Oct '17

19 Oct '17

> On Oct 18, 2017, at 2:07 AM, Yahui Yan <yahuiuk(a)gmail.com> wrote: > > Hi Elaine, > > I am a new user of chimeraX. I run it (the daily builds on 17th Oct 2017) in my Ubuntu system. All went well until I tried to save the session. An error message '[Errno 25] Inappropriate ioctl for device' popped out. Could you please give me some advice to fix it? Many thanks. > > Kind regards, > Yahui > Hi Yahui, I don’t know the answer, but I’m sharing it to the mailing list: chimerax-users(a)cgl.ucsf.edu … that is the recommended address for ChimeraX questions. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Fly function in ChimeraX
by Cheng, Tat 17 Oct '17

17 Oct '17

Hi, I have trying to make movies using Chimerax. But I am not sure I can find the command "fly" in Chimerax. Is there any replacement for the "fly" command? Thanks. Tat Cheng

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no distinguishing between capital and non-captital chain IDs in morph
by Haselbach, David 16 Oct '17

16 Oct '17

Hi everyone, I am using morph with same true to interpolate between two models. Unfortunately the models have each so many chains that there are capital and non capital letters used. The problem I have is, if I want to color the chains in the morph result I cant distinguish between capital and non capital chain ids anymore. So if I do "color #10/R green" not only chain R gets green but also chain r. I guess this is a bug. But is there a workaround? Best David

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mini info
by Bruno Villoutreix 02 Oct '17

02 Oct '17

Dear Colleagues do you think chimeraX could run on mac el capitan (10.11) or it requires the version above ? many thanks Bruno -- Dr. Bruno Villoutreix, PhD Structural Bioinformatics-Molecular Medicine, Chemoinformatics DR1 Inserm Head Inserm-Paris 7 Unit U973 Therapeutic molecules in silico (MTi) Inserm U973 - Lamarck Building 35 rue Helene Brion 75013 PARIS In silico tools and databases and more in my updated website : http://www.vls3d.com <http://www.vls3d.com/>

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Feature Request: Named selections
by Jared Adolf-Bryfogle 15 Sep '17

15 Sep '17

Hi All! I just started playing around with the alpha, and I’m very happy with it so far! Really love to windows and the ability to easily select models. One thing that is missing is a similar list of selections (yes, ala PyMol). I find these to be extremely useful in a long running session and I was wondering if something like that is planned. It would be similar to the model window, where you could control each selection and maybe apply view controls to each selection as well - like having components that are cartoon and others stick, etc. Thanks for any info! Sincerely, -Jared Jared Adolf-Bryfogle, Ph.D. Research Associate Lab of Dr. William Schief The Scripps Research Institute

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Fitmap enhancements?
by Oliver Clarke 14 Sep '17

14 Sep '17

Hi, fitmap can currently sequentially fit different models, but it would be really handy if fitmap could also sequentially fit parts of an individual model (in a single fitmap command). It would be great for a quick fit of a large complex if there was an `eachChain` and maybe `eachSegment` command, to sequentially fit each chain or each contiguous stretch of polypeptide. `eachSelection` would also be useful, allowing the user to give a list of atom selections for sequential fitting in fitmap. Cheers Oli

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Color palettes - ColorBrewer support?
by Oliver Clarke 12 Sep '17

12 Sep '17

Hi, I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)? It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc. It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet. Cheers Oli

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Re: [chimerax-users] [Chimera-users] 3D-SNFG symbol representation for carbohydrate molecules
by Eric Pettersen 06 Sep '17

06 Sep '17

Hi Oliver, We discussed this at the meeting today and the upshot is that we are very interested in doing this, but it will take us awhile to get to it. We intend to make a beta release of ChimeraX by the end of the year and there’s a lot of work to get done between then and now. Part of that work is to implement the “Nucleotides” representation that you see in regular Chimera but that isn’t yet available in ChimeraX. The “alternative atom depiction” that Nucleotides provides requires much of the same underlying support that showing the alternative carbohydrate depictions will require. Implementing Nucleotides first will allow us to iron out the issues involved in supplying that support and debug it. That will make implementing the 3D-SNFG representation much faster and improve its reliability. So we hope to be able to provide the carbohydrate depictions not long after the beta release date. I’d like to provide something faster, but as a practical matter I think this is the best we can do. I’m sure we will have questions about the details once we get onto the implementation, and hope you won’t mind if need to bug you a bit. :-) —Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 31, 2017, at 4:22 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > Dear Dr. Grant, > We are definitely interested, though we would be more likely to implement it in ChimeraX than Chimera, since most of our new work is in ChimeraX and also ChimeraX has better underlying support for adding new depictions like this. We will discuss this in a meeting on Tuesday and get back to you with further details. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Aug 31, 2017, at 7:18 AM, Oliver Grant <olivercgrant(a)gmail.com <mailto:olivercgrant@gmail.com>> wrote: >> >> Dear developers, >> >> The carbohydrate community has decided on a standard symbol representation for carbohydrates. The article is here <https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwv091>, and the webpage is here <https://www.ncbi.nlm.nih.gov/books/NBK310273/>. Our group has created a 3D version <http://glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-…> of the symbols within the software VMD. Here's a video showing both versions. <http://glycam.org/docs/othertoolsservice/wp-content/uploads/sites/15/2016/0…> We have also worked with David Sehnal to implement this into LiteMol, here is an example <https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/?loadFromCS=5a6z>. I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so. >> >> Regards, >> >> Dr. Oliver Grant >> Associate Research Scientist >> Complex Carbohydrate Research Center >> Athens, GA, USA. >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Not a software whiz!!!!!!!!!
by Arthur Szabo 05 Sep '17

05 Sep '17

Have downloaded ChimeraX as I would like to include a ribosome structure or part of it in my work. ChimeraX is, I am aware, largely a command based operational process. I feel like a real dummy because I do not understand how to achieve the imagery that I would like I have been able to open PDB 4WPO can rotate it and similar things, and there seem to be two molecules in the unit cell. I stumbled on a list of all the proteins, rRNAs and some other components in the structure such as EFG, an elongation factor. Can't figure out how to delete one of the model units from the image, as I was able to do with Chimera. I find it virtually impossible to understand the logic of the commands. Of course the command structure is similar to that in Chimera, but I only used that infrequently. I used the menu driven tools etc almost exclusively. I could achieve what I wanted with them and the learning curve was quite tolerable. Then when I got stuck I received excellent advice from Chimera staff on how to use the commands when needed. For example color spec<atomspec.html> colorname general-options What is the designation or meaning of spec ? How would I select the EGF protein from the ribosome to color it. 4wpo #1, chain DZ: 50S ribosomal protein L9,Elongation factor G. 4WPO is the pdb number, #1, I believe to one of the two units in the model. Chain DZ refers to the protein. I tried several permutations of this information and only received error messages. color<help:user/commands/color.html> 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword color<help:user/commands/color.html> red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G Expected one of 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword color<help:user/commands/color.html> ribbons red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword color<help:user/commands/color.html> ribbons red 4wpo #1, chain BZ Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword Colorname I think I understand, and I think that I have found a log of the different colors. Have no idea of what general-options might refer to. Here is more of my log. show<help:user/commands/show.html> selAtoms ribbons help<help:user/commands/help.html> help:user select<help:user/commands/select.html> 4wpo #1, chain BZ Expected an objects specifier or a keyword help<help:user/commands/help.html> help:contact.html help<help:user/commands/help.html> help:contact.html color<help:user/commands/color.html> #1 BZ red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword Similarly I can't understand what the terms in select spec<atomspec.html> [ polymer chain-spec<atomspec.html> ] might mean. The learning curve will be very much steeper than that for Chimera. Please allow me to make a suggestion. It would be useful to have a list with the definition of the terms used in the commands with clear examples. One example is spec another would be ref-spec or general-options I couldn't find one if it was there. These are only a few examples. Such terms are not defined anywhere. The persons most familiar with them are the persons who have written the programs, and those who have used the programs extensively. Some things like ( cartoon | ribbon ) atom-spec<atomspec.html> [ smooth factor | default ] [ suppressBackboneDisplay true | false ] appear to be well explained but again atom-spec is not defined nor an example given at least none that I could find. Kindly consider my comments as questions and friendly suggestions. I downloaded Pymol the other day, and couldn't get to first base. Would have to take a course on how to use it. I removed it from my computer. I don't have the time to learn even the basics about Pymol, and there are no clear explanations anywhere. I assume students learn from their colleagues who have spent considerable time learning the nuances of the program. I have a similar view of Photoshop - huge learning curve. Maybe an interactive course on YouTube video might be useful for ChimeraX Regards And thanks. AGS

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Re: [chimerax-users] Color protein by residue
by Elaine Meng 29 Aug '17

29 Aug '17

Hi Tom, Could you say more about what you mean about “collaborative” in terms of VR, what program(s) you used, how you controlled the display (e.g. typed commands to color and show/hide or something else like menus in the VR or voice control) or and whether you were looking at atomic details of proteins or just overall structures? (If you don’t want to send that info to the whole list, can just e-mail me individually.) For the most part, what we’ve done with ChimeraX is described here: <http://www.cgl.ucsf.edu/home/meng/chimerax/docs/user/vr.html> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > > Hi Elaine, > > Wow, your .cxc file works perfectly. Thanks for showing me how to do this, great help. > > On the VR stuff, yes, I’ve been using the VR on/off with our HTC Vive system. Works great if you keep the lighting effect simple. It is why I was suggesting your team take a look at what is possible in an immersive collaboration VR environment. I look forward to hearing from someone on your team. > > Best, and again thanks, > Tom >

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Color protein by residue
by Tom Skillman 28 Aug '17

28 Aug '17

I can’t figure out the command for coloring the proteins of a protein with standard colors.. Can you help? Thx. ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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Re: [chimerax-users] 4D imaging - metadata and time slider
by Mateusz Biesaga 23 Aug '17

23 Aug '17

Hi all, I use ChimeraX for 4D visualization and so far I am very satisfied with the results, thank you for this amazing tool! I have a two questions: - While presenting data that changes in time (xyt or xyzt as I do in Chimera) it is usually required to display the timing on the image. Is there a way to access the metadata and display it, possibly using 2dlabels function? I work particularly with TIFF files. - After I upgraded Chimera to second alpha release, I can see no time slider above the command line. I open my 4D data using asterisk in the filename, as described in tutorial: http://www.rbvi.ucsf.edu/chimera/data/light-apr2017/light4d.html Is there a new way of accessing this slider? Thanks, Mateusz

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ChimeraX alpha 2 release available
by Elaine Meng 17 Aug '17

17 Aug '17

Hi everybody, Earlier this week, we made a second alpha release of ChimeraX. It’s available in the download page, along with the earlier alpha release and the ongoing daily builds. <http://www.rbvi.ucsf.edu/chimerax/download.html> To help you decide when and if to update, we’ve also created a change log listing some of the more significant changes and when they occurred. We intend to keep adding to it as development proceeds. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Enjoy! Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Remote control?
by Simon Smith 24 Jul '17

24 Jul '17

I'm trying to find a way to mirror ChimeraX commands from one machine onto several others running on a network. Could someone tell me if the 'remotecontrol' command would be a good way to do this, and if so, how I could get started using it? As far as I can tell there's no documentation available for it yet. Thanks, Simon

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VR Features
by Fortney, Christopher (NIH/OD/ORS) [C] 21 Jul '17

21 Jul '17

Hello Chimera X Team, My name is Chris Fortney - I run the VR Program at the NIH Library. We've been using ChimeraX for VR demonstrations here for some time now, ever since James Tyrwhitt-Drake (3D Print Exchange, NIAID) and I first installed it here earlier this year. The word has spread at NIH - people like ChimeraX for VR! I was hoping I could just email you to introduce myself, and to give feedback on the main features that have been requested. The first being the ability to make selections and then view/add labels while in VR. The second being the ability to add additional cameras to the scene. This would be especially useful for mixed reality. We have a green screen here, and would love the ability to drop a 3rd camera into the scene for that. Being able to add additional cameras could be very useful to run multiple headsets in the same scene, so that two scientists could work on the same structure at the same time. Looking forward to hearing back, keep up the excellent work! It definitely has not gone unnoticed over here. Thanks, Chris Fortney

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Tool autostart
by Eric Pettersen 19 Jul '17

19 Jul '17

You can now control which tools are auto-started when ChimeraX starts by bringing up a context menu over the tool (typically by right clicking) and toggling “Start this tool at ChimeraX startup” on/off. This works for all tools/toolbars. It’s a little tricky for the Python shell tool in that that tool’s builtin context menu is pretty handy so we didn’t want to replace it. To control that tool’s autostart you have to position the mouse on the thin border that surrounds the type-in area and bring up a context menu there. That menu will have the autostart entry in it. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Saving PDB files
by Eric Pettersen 18 Jul '17

18 Jul '17

ChimeraX can now save PDB files. See the documentation for the ‘save’ command <http://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html> for details. You can also save PDB files from the File->Save dialog, but since the dialog does not yet display the command options, they will have their default values. That may be good enough in some cases. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimerax-users] [Chimera-users] Is it possible to dump out the SAS surface points calculated by ChimeraX?
by Elaine Meng 10 Jul '17

10 Jul '17

Hello Francois, (There is a chimerax-users e-mail list, CC’d here.) Note that the surface displayed in Chimera and ChimeraX is the SES, not the SAS. For spacing of points, see the “surface” command option “gridSpacing” — use ChimeraX command “help surface” or view the help at our website: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> Use ChimeraX command “save formats” to see what formats you can save. STL or X3D would include the surface vertices, I believe. For full details on “save” use command “help save” or see the copy here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.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 Jul 10, 2017, at 2:01 AM, Francois BERENGER <berenger(a)bioreg.kyushu-u.ac.jp> wrote: > > Hello, > I am not interested by surface normals, > the 3D coordinates would be enough. > > Is it possible to control the surface sampling of the surfacing algorithm? > Like with a number of points per Angstrom^2 parameter? > Thanks a lot, > Francois. >

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H bonds
by Eric Pettersen 30 Jun '17

30 Jun '17

ChimeraX can now find hydrogens bonds. The “hbonds” command is very similar to the same command in Chimera 1. The principal difference is that since ChimeraX uses cylinders instead of lines to depict the hydrogen bonds, the “lineType” and “lineWidth” keywords have been replaced with “dashes” and “radius” (and the hydrogen bonds are now dashed by default). Full details are available with “help hbonds” or at this link: http://www.cgl.ucsf.edu/chimerax/docs/user/commands/hbonds.html <http://www.cgl.ucsf.edu/chimerax/docs/user/commands/hbonds.html> Unfortunately, the hydrogen bond computation is also slower than in Chimera 1. We are working on that. —Eric Eric Pettersen UCSF Computer Graphics Lab

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From Arun: Request for information
by Arun Prasad Chopra 23 Jun '17

23 Jun '17

Dear Sir, I was using Chimerax software to identify the residues (aminoacids and nucleotide) that are interacting and also if we can know the binding energy of this transcription factor with DNA motif. I would be thankful for helping me identifying the residues. The PDB file is enclosed Thanks and Best Regards Arun -- Arun P. Chopra, Ph.D. Associate Prof., Department of Biotechnology Hindustan College of Science and Technology, Farha, Mathura 281 122 UP, India Cell # + 921 969 7932, 956 800 6057 http://hcst.edu.in/ http://www.sgei.org/

2 1

Cheat Sheet for ChimeraX
by Dan Echelman 20 Jun '17

20 Jun '17

Hi all, I'm just getting started on ChimeraX and was wondering if anyone had made a quick reference sheet for the commands? Thanks and best! Daniel

2 1

Initialzing core
by Hernando J Sosa 16 Jun '17

16 Jun '17

Dear ChimeraX team, I just downloaded/installed ChimeraX (64 for windows, latest daily build & PC running Windows 7) but when starting the programs hangs with the message Initializing Core and an image of the group (Nice picture though!). Anything I should do differently? (Chimera 11.2 runs fine in the same computer). Thanks Hernando

3 5

NoGUI mode?
by Simon Smith 16 Jun '17

16 Jun '17

Can someone tell me if the --nogui command is working currently? Trying one of the recent daily builds on my computer and ChimeraX refuses to launch if I add this flag. If there's some other way to get ChimeraX to display graphics without having toolbars and other windows on the side, please let me know. We're trying to get it to work in a multi monitor setup and being able to display the graphics only would be very helpful. Simon Smith

2 1

ChimeraX on Github?
by Tom Goddard 13 Jun '17

13 Jun '17

Oliver Clarke writes: Re this - dumb q, but have you considered moving to Github or similar for chimeraX? It would make it easier to know (as a user) whether a bug has been reported already or not, and perhaps also provide a way for you guys to quantify the perceived desirability of feature requests and bug fixes (which as you say the mailing list is not so good for). Loving the capacity to select atoms through maps in ChimeraX now by the way, it works really well! Cheers Oli

1 1

Getting stereo to work
by Simon Smith 09 Jun '17

09 Jun '17

Hello, We're trying to get ChimeraX to work with our sequential stereo setup (Quadro 5000, driver 369.26). Using the 'camera stereo' command always gives the error message 'Do not have stereo OpenGL context', even when using the --stereo command line flag. Setting the right stereo settings in Nvidia Control Panel hasn't made a difference either. Does anyone have any hints/ideas on how to get this to work? Thanks, Simon

3 5

Re: [chimerax-users] Inconsistencies in text entry behavior
by Tom Goddard 02 Jun '17

02 Jun '17

Hi Oliver, I see — when you click into the graphics pane and type a letter or number in Chimera 1, the command entry field takes the focus (you see it outlined) and the up arrow and down arrow keys traverse the command history. But in ChimeraX the command entry field does not take the focus, and up and down arrow promote the selection. I’m not sure which behavior is better, but I’ve made a ticket to possibly change ChimeraX to behave like Chimera. http://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/703 <http://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/703> Tom > On Jun 2, 2017, at 12:53 PM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: > > Ah yes - sorry Tom I misspoke - I was actually thinking specifically of the scenario where a residue is *not* selected. E.g. You are turning the model using the mouse, and you want to type a command altering display parameters - e.g. clipping and such. > > In this case, typing works fine in both chimera and chimeraX, but scrolling through the history using up or shift-up only works in chimera - in chimeraX you need to click on the command line such that a text cursor is visible. > > Oli > > On Jun 2, 2017, at 9:03 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > >> In Chimera or ChimeraX if you select a residue in the graphics window, you can then directly type a command. But if you press the up arrow or down arrow key it extends the selection to the whole helix or strand or turn, or demotes the selection — it does not allow you to traverse previous commands in the command-line. I just tested on Mac and it works that way on both. >> >> But maybe you mean you have clicked into some other ChimeraX panel, not the graphics window and then up / down arrows don’t traverse the command-line history or promote selection, although commands can be typed. For instance clicking into the ChimeraX log I suspect up/down arrow actually do something in that html panel, but I’m not sure what. In Chimera, clicking into the reply log blocks not only up/down arrow but all keys from going to the command line. So I don’t understand your case. But I believe the Qt window toolkit sometimes has default up/down arrow bindings on the panel you are clicked into that might not make sense. Explain your exact case and send it to chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> — probably better than the user mailing list. >> >> Tom >> >> >>> On Jun 2, 2017, at 12:33 AM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: >>> >>> Hi, >>> >>> The ChimeraX command line, similar to Chimera, is active no matter where the mouse cursor is positioned. So I can have a residue selected, and start typing a command directly - so far so good. >>> >>> However, in Chimera, once I start typing, I can then page through the command history, using the up arrow or shift-up to filter by substring. >>> >>> In ChimeraX, this doesn’t work - the command line receives text input, but in order to then page through the history, I need to actively click on the command line entry bar to activate it - it would be good if this behavior was altered to that of regular chimera. >>> >>> Apologies for the vague description, hope that made sense! >>> >>> Cheers >>> Oli >>> >>> >>> _______________________________________________ >>> 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

oddness with using right mouse button to adjust map contour
by Oliver Clarke 02 Jun '17

02 Jun '17

Hi, Using the right mouse button to adjust map contour works very well at volume step 2, but displays odd behavior at step 1. This may of course be a slow computer issue (MacBook pro 2015 13”, integrated graphics), but figured I’d report it in any case. Specifically what happens, is as I right click drag, the map contour appears to adjust correctly, but then when I release the mouse button, the map jerks back to a very low contour. Cheers Oli

2 1

Mesh lighting off?
by Oliver Clarke 02 Jun '17

02 Jun '17

Hi, Is there any way at present to turn mesh lighting off in ChimeraX? Cheers Oli

2 2

Inconsistencies in text entry behavior
by Oliver Clarke 02 Jun '17

02 Jun '17

Hi, The ChimeraX command line, similar to Chimera, is active no matter where the mouse cursor is positioned. So I can have a residue selected, and start typing a command directly - so far so good. However, in Chimera, once I start typing, I can then page through the command history, using the up arrow or shift-up to filter by substring. In ChimeraX, this doesn’t work - the command line receives text input, but in order to then page through the history, I need to actively click on the command line entry bar to activate it - it would be good if this behavior was altered to that of regular chimera. Apologies for the vague description, hope that made sense! Cheers Oli

1 0

XYZ format
by Mike Goodstadt 01 Jun '17

01 Jun '17

Hi! Many thanks for the great work on this new version. Does ChimeraX support XYZ files? Chimera did but I get an “unrecognized filetype” error in ChimeraX. Best regards, Mike Goodstadt mikegoodstadt(a)gmail.com skype: mikegoodstadt +34 653 756 614

3 6

Global toggle for volume/model display?
by Oliver Clarke 01 Jun '17

01 Jun '17

Hi, In old chimera, often I will have a few maps loaded, but only one or two specific ones displayed (and similarly for models). Frequently, I want to turn off the display of model information, in order to just see the desired map(s) or vice-versa, and then return to the original display, but there is no convenient way of doing this - I have to go to the volume viewer or model panel and check or uncheck the desired models. Would it be possible to add global toggles for the display of model/map information for this purpose, perhaps implemented as toolbar buttons? Cheers Oli

1 0

Re: [chimerax-users] Suggestion - add shortcuts for Ca trace, Ca+sidechains
by Tom Goddard 30 May '17

30 May '17

It seems that ChimeraX does not display CA traces — it shows just the atoms with no bonds between them. I see that CA-only structures do draw dashed lines between the CA atoms. I’ll have to ask Eric Pettersen on Tuesday what the plan is for depicting CA traces — apparently the mechanism that creates the pseudobonds between CA atoms automatically as is done in Chimera is not in ChimeraX. Tom > On May 26, 2017, at 10:03 AM, Oliver Clarke wrote: > > Sounds great!! > > Alternative - have a C-alpha trace button and show/hide side-chain/base button? > > That way if you do all atoms, you could quickly hide/show side chains, or if you’re displaying C-alpha trace and you want to quickly pop on side chains you can do so also? (Could also add this as a custom button of course) > > Cheers > Oli >> On May 26, 2017, at 1:00 PM, Tom Goddard wrote: >> >> Yes a C-alpha trace toolbar button would be nice — I’ll add that. The random atom color toolbar button is just for laughs — I’ll retire that one when I add C-alpha trace. The C-alpha trace plus side-chain doesn’t seem too different from full backbone + side chain in visual complexity, and backbone + sidechain already has a toolbar button (show all atoms). I’m thinking maybe that would be a toolbar button you could add as a customization. I plan to add a command soon where you can add new toolbar buttons (you specify and image file for icon and the command to execute using a command e.g. "toolbar add “CA trace” icon iconfile.png command "show selAtoms & @CA” shortcut ca” and it would be remembered in a preference file. Another useful one would be your thick backbone and thin side-chain sticks. >> >> Tom >> >> >>> On May 26, 2017, at 7:35 AM, Oliver Clarke wrote: >>> >>> Hi, >>> >>> Frequently when looking at models in medium resolution maps (~4-5 Å), it is valuable to view the C-alpha trace when assessing model map fit (or making figures to show such). >>> >>> At slightly higher resolution, where side chains are obvious but backbone torsions cannot be modeled based on the map alone, representing the C-alpha trace with sidechains displayed is often desirable (examples of both attached). >>> >>> It looks like there is space in the upper toolbar for additional buttons - perhaps adding a button for a Calpha trace representation (equivalent would be P for nuclei acids) and one for a Calpha+sidechain/base representation may be worth considering? (I’m also not convinced of the value of the random atom colors representation as a shortcut, but maybe there is a use case I’m missing?) >>> >>> Cheers >>> Oli >>> <Screenshot 2017-05-26 10.34.38.png><Screenshot 2017-05-26 10.34.25.png> >>> <Screenshot 2017-05-26 10.23.18.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

1 1

button for next/previous volume?
by Oliver Clarke 30 May '17

30 May '17

Hi, I frequently encounter the issue in “old” chimera where I have a bunch of different maps and I want to switch between them one by one, to better perceive differences or look at them in concert with another model. This is kind of tedious using the volume viewer, especially when many volumes are loaded concurrently Would it be possible to add next/previous volume buttons as shortcuts for this? I would envision this as follows: If multiple volumes are currently displayed, display the one with the lowest #ID and undisplay the rest. If a single volume is displayed, hide it and display the one with the next or previous ID (in a circular fashion, such that the next from the highest ID is the first ID. I have similar shortcuts in Coot which I use all the time and find very helpful for this purpose. Cheers Oli

2 1

Scale bar?
by Oliver Clarke 30 May '17

30 May '17

Hi, it would be nice (when using orthographic projection) to have the option of a dynamically updating scale bar integrated into the main display. This would be helpful when analyzing structures and also when making figures. Cheers Oli

2 2

Suggestion - add shortcuts for Ca trace, Ca+sidechains
by Oliver Clarke 26 May '17

26 May '17

Hi, Frequently when looking at models in medium resolution maps (~4-5 Å), it is valuable to view the C-alpha trace when assessing model map fit (or making figures to show such). At slightly higher resolution, where side chains are obvious but backbone torsions cannot be modeled based on the map alone, representing the C-alpha trace with sidechains displayed is often desirable (examples of both attached). It looks like there is space in the upper toolbar for additional buttons - perhaps adding a button for a Calpha trace representation (equivalent would be P for nuclei acids) and one for a Calpha+sidechain/base representation may be worth considering? (I’m also not convinced of the value of the random atom colors representation as a shortcut, but maybe there is a use case I’m missing?) Cheers Oli

2 1

UI suggestion - modifier key for map selection/interaction
by Oliver Clarke 25 May '17

25 May '17

Hi, Often I want to select or hover over (to reveal tooltip info) atoms located under a transparent surface or mesh. It is much less common to want to select a volume with ctrl-click in my experience. Would it be possible to add a modifier (e.g. Shift or alt/option) for volume selection, and otherwise default to selection of/interaction with the atomic model(s)? I feel like since ChimeraX deals mostly with these two data types, often in combination, having a clear way to distinguish interaction with them would be useful - it adds one extra step to be able to see atoms under a mesh, go to the volume viewer and turn of the required volume or volumes before selecting/identifying them - what do you think? Cheers Oli

2 1

Export silhouettes as SVG?
by Oliver Clarke 24 May '17

24 May '17

Hi, Probably low on the priority list, but I wonder if it would be possible in the future to add an option to export silhouettes (if present) in a vector format such as SVG? This would be incredibly useful when attempting to make realistic schematic figures, and creating scalable assets that can be reused in multiple figures, e.g. generic amino acids, lipids, surface representations of particular proteins, etc. Cheers Oli

3 2

Wire representation for models?
by Oliver Clarke 23 May '17

23 May '17

Hi, would it be possible to add wire representation to ChimeraX? Two reasons: 1: In regular Chimera, wire representation is much, much faster for rotation/translation for large models when clipping is enabled, so I find it useful to get the right view (before switching to another representation). This is probably due to the fact that I’m running Chimera on a MacBook pro with integrated graphics, but I think this is probably not so uncommon as a use case. 2: Even although it is old school and basic, for some purposes (e.g. in conjunction with mesh maps), I prefer this representation, as it has clean, simple lines which are nice for emphasizing connectivity/angles. Cheers Oli

2 1

Interactive map sharpening and filtering?
by Oliver Clarke 10 May '17

10 May '17

Hi, Has any consideration been given to adding the capacity for fourier-space map sharpening/low pass filtering to ChimeraX? I’m not sure whether or not it is feasible speed wise, but if it is it would be a very useful addition for EM, allowing one to easily try different sharpening B-factors/low pass cutoffs and save the resulting map(s). Cheers Oli

3 4

Change definitions of toolbar buttons?
by Oliver Clarke 09 May '17

09 May '17

Hi, Is it possible to change the definitions of toolbar buttons? Specifically, I’m thinking about the "save image” button, the idea of which I like very much, but which saves an image that is rather too low res for my taste. Can I redefine it so that it saves a higher quality image? More generally, will it be possible to create custom toolbar buttons, which execute an arbitrary ChimeraX command? Cheers Oli

2 2

Hotkeys?
by Oliver Clarke 09 May '17

09 May '17

Hi all, Loving ChimeraX! It has got a lot faster on Mac with integrated graphics than the last time I tried it, and I *love* the curved helices and ambient occlusion lighting! UI seggestion: Would it be possible to allow users to define custom hotkeys to execute particular functions? E.g. swapping between preset display settings, adjusting the contour level of a selected volume, switching the view, etc? Hotkeys have an advantage over command line entries that they are faster and can’t be mis-typed. This idea would require a slight tweaking of how the command line works, such that you can only enter commands when the command line is active, but I don’t think this would be such a bad thing. One could also have a hotkey to activate the command line (e.g. Tab or Ctrl-T). I feel like this would allow expansion and customization of the interface in useful ways. With regards to the command line, would it be possible to add in tab-completion of commands, like one has in a bash shell? Although the documentation is extensive, I feel like this might improve the discoverability of various commands, and would certainly make them faster to type. Keep up the good work, looking forward to seeing what’s coming next! Cheers Oli

2 1

Simple programming features in ChimeraX command language?
by Oliver Clarke 08 May '17

08 May '17

Hi, Is there any possibility of adding simple scripting features to the ChimeraX command syntax in the future? Obviously more complex things will be done in a python script, but if/then/for/while statements would be very handy to add to the power of one liners and aliases on the command line - e.g. for each chain in molecule1, if chain is protein, fit to map, things like that? Cheers Oli

2 2

Rapid access panel suggestions
by Oliver Clarke 07 May '17

07 May '17

Hi, Rapid access panel looks great and is very helpful! Would be great to have a check button to filter by filetype (or at least structure/volume data), an option to switch between list/icon view, and perhaps a text entry box to filter on a typed substring of the filename. Cheers Oli

1 0

animations
by Giorgio Luciano 01 May '17

01 May '17

Hello ! In the effort to create a more integrated pipeline with vastly used 3d software (I use mainly C4D and modo) is there a way to export animation from chimera in a format that other software can interpret. To make an example. If I wiggle a molecule in chimera, can I export the animation in a format that does not lot this info ? And eventually are there plan to create this feature in chimeraX ? Giorgio

3 6

iPad?
by Villa, Elizabeth 24 Apr '17

24 Apr '17

Hi, I'm wondering if plans to make a Chimera version for the iPad. I think that it will be very valuable for scientific conferences, etc. Thanks in advance, Elizabeth Sent from my mobile device. Please pardon brevity and any typos.

2 1

Chimera bug report submission
by shumaila 18 Apr '17

18 Apr '17

Hi, I want to add oxygen molecule to iron atom in chimera . Kindly help me out how should I add O2 molecule? I tried by Addd bond option but the oxygen molecule is not attached at the desired place. Attached is the protein complex to which I want to attach O2 molecule.Kindly find the attachment. Thank You File attachment: pro time_15000ps.pdb

1 0

ChimeraX with NiceDCV
by Friedrich Foerster 11 Apr '17

11 Apr '17

Dear ChimeraX list, does anybody have experience with installing and running ChemiraX on remote desktop? we want to use it with NiceDCV. Thanks and best wishes friedrich -- prof. dr. Friedrich Foerster Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands Tel: +31 30 253 4318 http://www.uu.nl/en/research/cryo-em

2 1

"Rapid Access"
by Eric Pettersen 07 Apr '17

07 Apr '17

Hi all, In the latest builds, your file history will be shown in the main graphics area if there are no models open (e.g. usually at startup). Otherwise, you can hide/show the file list with the lightning bolt icon at the lower right of the main window. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

color zones in cryoem density map
by Jonas Barandun 05 Apr '17

05 Apr '17

Dear chimeraX users/developers Is there an easy way to color a cryoem density map based on individual subunits (from a pdb file) - similar to the color zone functionality in chimera? Thanks a lot Best Jonas

2 2

Chimera for 4D imaging analysis
by John Daum 05 Apr '17

05 Apr '17

Ladies and Gents, I recently heard a talk at Janelia Research Campus's "Frontiers in Imaging Science" given by Dyche Mullins, an investigator at USCF. He heaped praise upon Chimera/ChimeraX and indicated that it had been adapted for working with 4D light microscopy images that might be quite useful for quantifying and or viewing objects in 3D space over time by surface rendering and other cool "tricks". I'm writing to inquire if Chimera, ChimeraX, or another version (perhaps currently unavailble for download from the UCSF Chimera website) will help me with my problem (analyzing, viewing, 4D data)? Thank you, John Daum Laboratory Manager, Gorbsky Lab, Bell 216 Cell Cycle and Cancer Biology Oklahoma Medical Research Foundation 825 N. E. 13th Street Oklahoma City, OK 73104 daumj(a)omrf.org Voice: 405-271-2037 Fax: 405-271-7312

2 1

ChimeraX announce list?
by Steffen Graether 05 Apr '17

05 Apr '17

I realize that traffic is very low on the Chimerax-users list, but is there any thought about adding an announce list so that we could follow announcements on new releases as development progresses? Steffen

2 2

chimeraX and nice dcv
by Beck, Florian 03 Apr '17

03 Apr '17

Hi, did anyone use chimerX with nice dcv remote visualisation ? I tried it and I got the following error: Could not connect to DCVD [13619:13619:0403/144451:FATAL:zygote_host_impl_linux.cc(182)] Check failed: ReceiveFixedMessage(fds[0], kZygoteBootMessage, sizeof(kZygoteBootMessage), &boot_pid). #0 0x2ada6e6ec00e <unknown> #1 0x2ada6e6ff0ce <unknown> #2 0x2ada6ec92e33 <unknown> #3 0x2ada6ec91b2b <unknown> #4 0x2ada6ec920ce <unknown> #5 0x2ada6ed09a69 <unknown> #6 0x2ada6eb13373 <unknown> #7 0x2ada6d5b1d32 <unknown> #8 0x2ada6d5b2f45 <unknown> #9 0x2ada6d555345 QtWebEngineCore::BrowserContextAdapter::BrowserContextAdapter() #10 0x2ada6cc8b75a QWebEngineProfile::QWebEngineProfile() #11 0x2ada6ca4cfc9 sipQWebEngineProfile::sipQWebEngineProfile() #12 0x2ada6ca4d1aa init_type_QWebEngineProfile #13 0x2ada6be5061b sipSimpleWrapper_init #14 0x2ada01ad1e83 type_call #15 0x2ada01a613fb _PyObject_FastCallDict #16 0x2ada01b51ae8 call_function #17 0x2ada01b5757a _PyEval_EvalFrameDefault #18 0x2ada01b5199a _PyEval_EvalCodeWithName #19 0x2ada01b5a7b8 _PyFunction_FastCallDict #20 0x2ada01a614fe _PyObject_FastCallDict #21 0x2ada01a61602 _PyObject_Call_Prepend #22 0x2ada01a6129a PyObject_Call #23 0x2ada01b56ffb _PyEval_EvalFrameDefault #24 0x2ada01b5199a _PyEval_EvalCodeWithName #25 0x2ada01b51c37 call_function #26 0x2ada01b570d1 _PyEval_EvalFrameDefault #27 0x2ada01b5199a _PyEval_EvalCodeWithName #28 0x2ada01b5a848 _PyFunction_FastCallDict #29 0x2ada01a614fe _PyObject_FastCallDict #30 0x2ada01a61602 _PyObject_Call_Prepend #31 0x2ada01a6129a PyObject_Call #32 0x2ada01ad96e9 slot_tp_init #33 0x2ada01ad1e83 type_call #34 0x2ada01a613fb _PyObject_FastCallDict #35 0x2ada01b51ae8 call_function #36 0x2ada01b5757a _PyEval_EvalFrameDefault #37 0x2ada01b50ff0 _PyFunction_FastCall #38 0x2ada01b5a9e0 _PyFunction_FastCallDict #39 0x2ada01a614fe _PyObject_FastCallDict #40 0x2ada01a61602 _PyObject_Call_Prepend #41 0x2ada01a6129a PyObject_Call #42 0x2ada01ad96e9 slot_tp_init #43 0x2ada01ad1e83 type_call #44 0x2ada01a6129a PyObject_Call #45 0x2ada01b56ffb _PyEval_EvalFrameDefault #46 0x2ada01b5199a _PyEval_EvalCodeWithName #47 0x2ada01b51c37 call_function #48 0x2ada01b570d1 _PyEval_EvalFrameDefault #49 0x2ada01b5199a _PyEval_EvalCodeWithName #50 0x2ada01b51c37 call_function #51 0x2ada01b570d1 _PyEval_EvalFrameDefault #52 0x2ada01b5199a _PyEval_EvalCodeWithName #53 0x2ada01b51f5f PyEval_EvalCodeEx #54 0x2ada01a92dae function_call #55 0x2ada01a6129a PyObject_Call #56 0x2ada01b56ffb _PyEval_EvalFrameDefault #57 0x2ada01b5199a _PyEval_EvalCodeWithName #58 0x2ada01b51c37 call_function #59 0x2ada01b5757a _PyEval_EvalFrameDefault #60 0x2ada01b50ff0 _PyFunction_FastCall #61 0x2ada01b51efd call_function Fatal Python error: Aborted Current thread 0x00002ada01821600 (most recent call first): File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/ui/widgets/htmlview.py", line 70 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/ui/widgets/htmlview.py", line 164 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/tool.py", line 124 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/tool.py", line 172 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/tools.py", line 181 in get_singleton File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/cmd.py", line 19 in get_singleton File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/__init__.py", line 30 in start_tool File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/toolshed/__init__.py", line 2051 in start_tool File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/tools.py", line 387 in start_tools File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/tools.py", line 364 in autostart File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/ChimeraX_main.py", line 454 in init File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/ChimeraX_main.py", line 643 in <module> File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/runpy.py", line 85 in _run_code File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped) best Florian

2 1

Re: [chimerax-users] Tubes
by Tom Goddard 03 Apr '17

03 Apr '17

Hi Martin, That is odd, I didn’t know the helix cylinder diameters varied in ChimeraX. I don’t know the algorithm or how to change the diameter. Maybe Conrad (who wrote the code) or Elaine will know. There is a chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list that you can ask such questions on. Tom > On Apr 3, 2017, at 10:40 AM, Martin Moncrieffe wrote: > > Hi Tom, > > When displaying helices as tubes, can one set the radius of the tubes? I’ve noticed that depending on the structure, the tube diameter is scaled scaled differently even though the docs state that w/h/x-secton do not apply in tube mode. I’m sure you guys have some fancy algorithm to do so. > > Anyway, I really like what you’re all doing so far. > > Best. > > __martin > >

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Hello everyone
by Bagaruwa Danjuma 28 Mar '17

28 Mar '17

Please I tried several times to download ChimeraX but I kept receiving the following message: Not Found The requested URL /chimerax/download.html was not found on this server. ------------------------------ Apache/2.4.6 (CentOS) Server at www.cgl.ucsf.edu Port 443 What do I do to get it downloaded. Thank you very much. Abubakar

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ChimeraX Alpha release
by Eric Pettersen 28 Mar '17

28 Mar '17

Hi all, We have released an alpha version of ChimeraX. While it still lacks many features, it has enough useful new and fun features that you might want to take it out for a spin even if it doesn’t prove ready to be your day-to-day workhorse yet. Hope you like it! Home page: http://www.cgl.ucsf.edu/chimerax/ <http://www.cgl.ucsf.edu/chimerax/> Download page: http://www.cgl.ucsf.edu/chimerax/download.html <http://www.cgl.ucsf.edu/chimerax/download.html> —Eric Eric Pettersen UCSF Computer Graphics Lab

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Opening X3D?
by Aaron Lewis 28 Feb '17

28 Feb '17

Dear x-users, I've tried to open x3d files using recent Mac and Linux dailies, but without any success. This would be useful as a way to view maps colored in Chimera 1 & Segger. I take it from docs/user/commands/open.html that the following usage should be supported: open ~/Desktop/color.x3d format x3d but I only get the error below. Any suggestions would be welcome. Aaron -- Traceback (most recent call last): File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/tool.py", line 158, in execute cmd.run(cmd_text) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2257, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 108, in open models = session.models.open(paths, format=format, name=name, **kw) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 351, in open session, filenames, format=format, name=name, **kw) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 368, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 298, in open_data open_func = fmt.open_func AttributeError: 'NoneType' object has no attribute 'open_func'

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application does not work
by Mikhail G 02 Feb '17

02 Feb '17

Dear sir/madam: I downloaded and installed chimerax 01 at windows 7 (Norton antivirus). It was installed OK, however when i try running a program it blinks and quits. What to do? i reinstalled it 2 times. MG

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Porting Chimera 1 extensions to ChimeraX
by Tom Goddard 12 Jan '17

12 Jan '17

Hi Matt, We don’t have a guide to porting Chimera 1 extensions to ChimeraX yet. We have not yet even made an alpha release of ChimeraX, and have just one outside developer who is writing a new extension rather than porting an old one. We will be providing info on porting extensions in the future. A major ChimeraX goal is to improve support for extension developers. Here are some basics about porting. 1) Chimera 1 uses the Tk window tookit for dialogs, menus, buttons, … while ChimeraX uses the Qt toolkit. 2) All attributes of molecules and maps are accessible from Python in both Chimera 1 and ChimeraX. 3) Methods for density maps are mostly identical in Chimera 1 and ChimeraX. 4) Methods for molecules, atoms, residues are mostly the same but with some changes (e.g. alt locs are different, chain ids can be longer than 1 character …) 5) To get better performance operating on large numbers of atoms there are new numpy array based methods to change atom attributes. 6) The packaging of an extension is different. Chimera 1 uses a ChimeraExtension.py file. ChimeraX uses Python wheels and a online distribution site called Tool Shed, https://cxtoolshed.rbvi.ucsf.edu <https://cxtoolshed.rbvi.ucsf.edu/>, and ChimeraX menu Tools / General / Toolshed allows one click installs of any tools. 7) Chimera 1 did not provide programming API documentation, while ChimeraX has API documentation http://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html <http://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html> 8) Chimera 1 used Python 2, ChimeraX uses Python 3. Python 3 import statements and print statements are different and integer divide produces a float, but mostly it is the same. Most Chimera 1 extensions have a graphical user interface in Python / Tk that is often a lot of the code. Now we use Python / Qt because support for Tk is poor. Qt is totally different so all graphical user interface will have to be rewritten. Tom > On Jan 12, 2017, at 11:51 AM, Dougherty, Matthew T wrote: > > Hi Tom, > > Are there any guidelines, docs or examples as to converting extensions into chimeraX? > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > =================================================

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Re: [chimerax-users] obj export ? other 3d format ?
by Tom Goddard 04 Jan '17

04 Jan '17

Hi Giorgio, Thanks for the explanation. So Maya and Cinema4d can’t directly read Collada with vertex colors and preserve the coloring? Chimera uses vertex colors instead of textures for multicolor surfaces. Can your meshlab file conversion process work with the X3D output from Chimera and ChimeraX? I know X3D is not very well supported. What advantage do you see in using ChimeraX instead of Chimera for this model export? ChimeraX has completely reliable surface calculation where Chimera fails for large molecules. There is a semi-secret Chimera option to the surface command “grid 0.5” that makes Chimera use the reliable surface calculation from ChimeraX but the resulting surface is not associated with the atoms that generated it so copying colors from the atoms is more difficult (need to use the Chimera Color Zone tool). ChimeraX has nice ambient occlusion lighting that Chimera lacks, but that is not exported in scene files. Tom > On Jan 4, 2017, at 11:14 AM, Giorgio Luciano wrote: > > Hello thanks for the reply. So the idea is this. Genrally I need to import molecules in other software (maya+renderman, cinema4d+arnold). One of the problem I had was to "save" in some way the information of the materials of the models. Let's say I have calculated a properties of my molecule and I wanted to code it in the color (hydrophobicity for example, a particular charge density and so on). So since it was not easy to mantain it I generally did the following > 1) save as dae > 2) import in meshlab > 3) create a blank texture and then color the texture from the info in the vertex texture. > In this way I can then export the info in all the software I want (including zbrush for example and so use subsequently KEYSHOT for a fast cool render). > If needed I can create a small video about that :) > Now the problem is that I cannot do it anymore in the new chimera :) So every format that can save the model+colors would be perfect. DAE seems the one to work better for now (can be imported withouth loss in meshlab and blender) > Thanks for creating such a great software :) > Giorgio > > Il giorno mar 3 gen 2017 alle ore 20:46 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> ha scritto: > Hi G, > > ChimeraX will eventually export OBJ and Collada 3d formats but we don’t have a schedule for that. It currently exports STL for use with 3d printers (single color). We also can save X3D, again added for 3d printers (multi-color). Some ChimeraX code (cellPACK tool) reads Collada, but does not write it, but the PyCollada library is in ChimeraX so that is a start towards writing it. We have a hundred different features we want to get into ChimeraX eventually and their priority depends on how compelling the use is. It would help if you told us why you want OBJ and Collada export, and why it is an advantage to get it into ChimeraX versus using the current capability in Chimera 1. > > Tom > > > > > On Dec 29, 2016, at 11:01 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com <mailto:giorgio.luciano@gmail.com>> wrote: > > > > Dear all, just a message to ask if in CHIMERA X is on the roadmap an obj, dae export. > > G. > > _______________________________________________ > > 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> >

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obj export ? other 3d format ?
by Giorgio Luciano 29 Dec '16

29 Dec '16

Dear all, just a message to ask if in CHIMERA X is on the roadmap an obj, dae export. G.

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Testing 2
by Conrad Huang 16 Dec '16

16 Dec '16

Please ignore

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Testing
by Conrad Huang 16 Dec '16

16 Dec '16

Please ignore

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