July 2017 - ChimeraX-users - RBVI Mailing Lists

Remote control?
by Simon Smith 24 Jul '17

24 Jul '17

I'm trying to find a way to mirror ChimeraX commands from one machine onto several others running on a network. Could someone tell me if the 'remotecontrol' command would be a good way to do this, and if so, how I could get started using it? As far as I can tell there's no documentation available for it yet. Thanks, Simon

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VR Features
by Fortney, Christopher (NIH/OD/ORS) [C] 21 Jul '17

21 Jul '17

Hello Chimera X Team, My name is Chris Fortney - I run the VR Program at the NIH Library. We've been using ChimeraX for VR demonstrations here for some time now, ever since James Tyrwhitt-Drake (3D Print Exchange, NIAID) and I first installed it here earlier this year. The word has spread at NIH - people like ChimeraX for VR! I was hoping I could just email you to introduce myself, and to give feedback on the main features that have been requested. The first being the ability to make selections and then view/add labels while in VR. The second being the ability to add additional cameras to the scene. This would be especially useful for mixed reality. We have a green screen here, and would love the ability to drop a 3rd camera into the scene for that. Being able to add additional cameras could be very useful to run multiple headsets in the same scene, so that two scientists could work on the same structure at the same time. Looking forward to hearing back, keep up the excellent work! It definitely has not gone unnoticed over here. Thanks, Chris Fortney

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Tool autostart
by Eric Pettersen 19 Jul '17

19 Jul '17

You can now control which tools are auto-started when ChimeraX starts by bringing up a context menu over the tool (typically by right clicking) and toggling “Start this tool at ChimeraX startup” on/off. This works for all tools/toolbars. It’s a little tricky for the Python shell tool in that that tool’s builtin context menu is pretty handy so we didn’t want to replace it. To control that tool’s autostart you have to position the mouse on the thin border that surrounds the type-in area and bring up a context menu there. That menu will have the autostart entry in it. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Saving PDB files
by Eric Pettersen 18 Jul '17

18 Jul '17

ChimeraX can now save PDB files. See the documentation for the ‘save’ command <http://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html> for details. You can also save PDB files from the File->Save dialog, but since the dialog does not yet display the command options, they will have their default values. That may be good enough in some cases. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimerax-users] [Chimera-users] Is it possible to dump out the SAS surface points calculated by ChimeraX?
by Elaine Meng 10 Jul '17

10 Jul '17

Hello Francois, (There is a chimerax-users e-mail list, CC’d here.) Note that the surface displayed in Chimera and ChimeraX is the SES, not the SAS. For spacing of points, see the “surface” command option “gridSpacing” — use ChimeraX command “help surface” or view the help at our website: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> Use ChimeraX command “save formats” to see what formats you can save. STL or X3D would include the surface vertices, I believe. For full details on “save” use command “help save” or see the copy here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 10, 2017, at 2:01 AM, Francois BERENGER <berenger(a)bioreg.kyushu-u.ac.jp> wrote: > > Hello, > I am not interested by surface normals, > the 3D coordinates would be enough. > > Is it possible to control the surface sampling of the surfacing algorithm? > Like with a number of points per Angstrom^2 parameter? > Thanks a lot, > Francois. >

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