- ChimeraX-users - RBVI Mailing Lists

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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