- ChimeraX-users - RBVI Mailing Lists

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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color zones in cryoem density map
by Jonas Barandun 06 Apr '17

06 Apr '17

Dear chimeraX users/developers Is there an easy way to color a cryoem density map based on individual subunits (from a pdb file) - similar to the color zone functionality in chimera? Thanks a lot Best Jonas

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Chimera for 4D imaging analysis
by John Daum 05 Apr '17

05 Apr '17

Ladies and Gents, I recently heard a talk at Janelia Research Campus's "Frontiers in Imaging Science" given by Dyche Mullins, an investigator at USCF. He heaped praise upon Chimera/ChimeraX and indicated that it had been adapted for working with 4D light microscopy images that might be quite useful for quantifying and or viewing objects in 3D space over time by surface rendering and other cool "tricks". I'm writing to inquire if Chimera, ChimeraX, or another version (perhaps currently unavailble for download from the UCSF Chimera website) will help me with my problem (analyzing, viewing, 4D data)? Thank you, John Daum Laboratory Manager, Gorbsky Lab, Bell 216 Cell Cycle and Cancer Biology Oklahoma Medical Research Foundation 825 N. E. 13th Street Oklahoma City, OK 73104 daumj(a)omrf.org Voice: 405-271-2037 Fax: 405-271-7312

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ChimeraX announce list?
by Steffen Graether 05 Apr '17

05 Apr '17

I realize that traffic is very low on the Chimerax-users list, but is there any thought about adding an announce list so that we could follow announcements on new releases as development progresses? Steffen

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