- ChimeraX-users - RBVI Mailing Lists

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

12 Feb '20

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

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

11 Feb '20

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

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Reproduce exact view
by Christophe Leterrier 10 Feb '20

10 Feb '20

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

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

07 Feb '20

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

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

07 Feb '20

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

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

04 Feb '20

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

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Chimerax on a HPC cluster
by Thu Nguyen 31 Jan '20

31 Jan '20

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

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question about ChimeraX Hide Dust Feature
by Philip Schmiege 29 Jan '20

29 Jan '20

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

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

29 Jan '20

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

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

28 Jan '20

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

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volume morph
by Karim Rafie 28 Jan '20

28 Jan '20

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

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

28 Jan '20

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

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SMILES structures
by Eric Pettersen 27 Jan '20

27 Jan '20

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

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dome camera mode
by James Hedberg 24 Jan '20

24 Jan '20

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

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

24 Jan '20

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

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PubChem
by Eric Pettersen 22 Jan '20

22 Jan '20

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

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

21 Jan '20

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

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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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