- ChimeraX-users - RBVI Mailing Lists

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 10 May '17

10 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 10 May '17

10 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 09 May '17

09 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 19 Apr '17

19 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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"Rapid Access"
by Eric Pettersen 07 Apr '17

07 Apr '17

Hi all, In the latest builds, your file history will be shown in the main graphics area if there are no models open (e.g. usually at startup). Otherwise, you can hide/show the file list with the lightning bolt icon at the lower right of the main window. —Eric Eric Pettersen UCSF Computer Graphics Lab

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