December 2019 - ChimeraX-users - RBVI Mailing Lists

Starting ChimeraX programmatically with remotecontrol
by Mungo Carstairs (Staff) 11 Dec '19

11 Dec '19

Hi there, Jalview has the ability to launch Chimera with "--start RESTServer", capture the port number from the response, and drive Chimera with REST commands. I'm trying to figure out whether this mechanism is also provided with ChimeraX. I've read http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-July/000113.html and looked at http://www.rbvi.ucsf.edu/chimerax/docs/user/startup.html and http://www.rbvi.ucsf.edu/chimerax/docs/user/options.html#start but so far I can't see that "RESTServer" is a startable tool. Is this, or is it planned to be, possible somehow? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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Rotate bond move large/small option in VR
by Lewandowski, Jozef 09 Dec '19

09 Dec '19

Hi, Is there a way to change the option from the default “move small” to “move large” of the Bond rotation tool in VR? Ideally, it would be great if I could switch between these options on the fly with some combination of buttons on the controllers. If nothing like that is implemented is there a way I could change the “move” default for the Bond rotation tool in VR using the command line? Thanks, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

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Relative paths to source files in saved sessions
by Christophe Leterrier 04 Dec '19

04 Dec '19

Hi, I'm working on multiple Chimera sessions on different computers, syncing the content of the folders and cxs files. However when opening a cxs file on a different computer, I have to manually relocate all the source files every time (in my case tif stacks, and even navigate for each of them from the cxs folder to the source files folder because the folder is reset at every source file selection). Would it be possible to somehow store the relative path between the cxs file and the source files in the cxs file, or try relative if absolute paths fail? I have no idea how this is done currently, so sorry if this is an unrealistic/undesirable proposal. Thank you, Christophe

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Main interface does not start
by Thomas G. Laughlin III 04 Dec '19

04 Dec '19

Hi, I've been using ChimeraX 0.9 for a while, but today when I tried to open it, the group photo comes up and "initializing bundles" then disappears without starting the main interface/GUI. I recently installed items from the toolshed for the first time (2 days ago but ChimeraX worked the day of install) and I tried re-installing ChimeraX without success. This is on a Windows 10 OS with intel integrated graphics. Any suggestions on what to do to diagnose and correct the problem? Thanks for the help, -Tom -- Thomas G. Laughlin III PhD MCB (BBSB, Candidate) | *Univ. of California-Berkeley* | Present BS Biochemistry | *Univ. of Missouri-Columbia* | 2014 t.laughlin(a)berkeley.edu <thomas.laughliniii(a)gmail.com>

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Fw: Multi-user sessions: development
by Williams, Joanne 02 Dec '19

02 Dec '19

________________________________ From: Grime, John M. <jgrime(a)ou.edu> Sent: Monday, December 2, 2019 1:12 PM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Multi-user sessions: development Hello! We have some use cases where multi-user VR sessions in ChimeraX would be very useful. We already have out own in-house networked VR software, and I was wondering if the source code to ChimeraX is available for academic users so we can see if we can add similar functionality? Thanks! John Grime, Ph.D. Emerging Technologies Developer University of Oklahoma Libraries

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Double and Triple Bond Stick Style
by Smith, Chase 02 Dec '19

02 Dec '19

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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ChimeraX-users December 2019