- ChimeraX-users - RBVI Mailing Lists

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

21 Jan '20

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

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

21 Jan '20

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

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

21 Jan '20

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

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Tile a vseries
by Sean Connell 17 Jan '20

17 Jan '20

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

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

17 Jan '20

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

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

16 Jan '20

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

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

14 Jan '20

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

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Show dashed lines after hiding atoms
by Ahmad Khalifa 09 Jan '20

09 Jan '20

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

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

08 Jan '20

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

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

07 Jan '20

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

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

07 Jan '20

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

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differentiating file category
by Anthony James Schaefer 02 Jan '20

02 Jan '20

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

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Superimposition of Carbohydrate Molecules
by Rajarshi Roy 18 Dec '19

18 Dec '19

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

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Amber trajectories
by Lewandowski, Jozef 16 Dec '19

16 Dec '19

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

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

16 Dec '19

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

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SSL expiry
by James Walshe 13 Dec '19

13 Dec '19

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

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

12 Dec '19

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

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

11 Dec '19

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

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

11 Dec '19

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

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

09 Dec '19

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

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

04 Dec '19

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

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

04 Dec '19

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

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Fw: Multi-user sessions: development
by Williams, Joanne 02 Dec '19

02 Dec '19

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

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

29 Nov '19

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

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

27 Nov '19

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

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Color key
by Ricardo Righetto 18 Nov '19

18 Nov '19

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

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

11 Nov '19

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

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

06 Nov '19

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

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Catalina woes
by ubaumann 05 Nov '19

05 Nov '19

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

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

18 Oct '19

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

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problem of chimerax
by 陈柳青 18 Oct '19

18 Oct '19

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

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macOS Catalina gives PermissionError opening files
by Tom Goddard 15 Oct '19

15 Oct '19

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

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

14 Oct '19

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

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

14 Oct '19

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

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

14 Oct '19

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

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

09 Oct '19

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

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Unable to use Viewdockx
by Abhijeet Kumar 07 Oct '19

07 Oct '19

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

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Cuved helix tubes
by Ernesto Arias Palomo 02 Oct '19

02 Oct '19

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

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

02 Oct '19

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

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

25 Sep '19

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

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ray tracing
by Ahel,Juraj 24 Sep '19

24 Sep '19

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

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Manually imposed symmetry
by Shahid Khan 16 Sep '19

16 Sep '19

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

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render buriedArea surface?
by Alexis Rohou 09 Sep '19

09 Sep '19

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

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vdw representation in chimeraX
by Elena Zehr 09 Sep '19

09 Sep '19

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

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

05 Sep '19

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

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

03 Sep '19

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

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silhouette of transparent density
by YAO HE 30 Aug '19

30 Aug '19

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

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silhouette of transparent density
by heyao 30 Aug '19

30 Aug '19

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

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

28 Aug '19

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

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

21 Aug '19

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

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