May 2017 - ChimeraX-users - RBVI Mailing Lists

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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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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