- ChimeraX-users - RBVI Mailing Lists

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

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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

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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

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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> >>> >>

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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

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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

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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

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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

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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

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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 >> > >

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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.

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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

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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

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