- ChimeraX-users - RBVI Mailing Lists

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

03 Mar '20

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

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Bug: selection of atoms by attribute = color
by Pavol Bardy 393791 27 Feb '20

27 Feb '20

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

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change residues to helix
by Meinan Lyu 24 Feb '20

24 Feb '20

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

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

20 Feb '20

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

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Error in reopening session
by Maximiliane Wieland 20 Feb '20

20 Feb '20

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

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Set view
by Aritz Roa Eguiara 19 Feb '20

19 Feb '20

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

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undo/redo move?
by Oliver Clarke 18 Feb '20

18 Feb '20

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

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workflow suggestions
by Joel Meyerson 17 Feb '20

17 Feb '20

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

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

14 Feb '20

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

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Reverse color byhet
by Ahmad Khalifa 13 Feb '20

13 Feb '20

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

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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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