[chimerax-users] [EXTERNAL] Re: suggestion

Tue Nov 22 11:34:31 PST 2022

Thank you, Tom,
the 'rotate independent' command works as expected; same for the spacing (sorry I missed it in the doc).
So, everything was in place already!
Best Regards
s

_____________________________________
Sergio A. Hassan
https://bioinformatics.niaid.nih.gov/cmm/
BCBB/NIAID/NIH/DHHS
301 761 7221 (office) 301 741 5579 (mobile)

________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Tuesday, November 22, 2022 2:07 PM
To: Hassan, Sergio (NIH/NIAID) [E] <hassan at mail.nih.gov>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [chimerax-users] suggestion

Hi Sergio,

  To make ChimeraX rotate each displayed model about its own center you use the "rotate independent" mouse mode.  The tile command enables that mode.  You can enable it after loading a session with command

mouse left "rotate independent"

Loading a session file does not restore the mouse modes to what they were when you saved the session.  Maybe it should.  In this case it would be helpful but if you were using some other special purpose mouse mode I suspect you usually don't want the session file to remember that.  I've made a feature request to consider saving mouse modes in session files.

    https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8067#ticket<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8067%23ticket&data=05%7C01%7Chassan%40mail.nih.gov%7C4e760211d6d04552c9c408daccbcc67c%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638047409027378838%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=VJIK0PawXHwIIJzPfau8nFDbO%2Fkl6V9tkErOP3iEMxk%3D&reserved=0>

We'll add to the tile command documentation the above command which reenables the independent center of rotation.

  The tile command has an option to control the spacing between models called spacingFactor.  If you type command "usage tile" it will show you all the options

usage tile
tile [models] [columns an integer] [spacingFactor a number] [viewAll true or false] [independentRotation true or false]
    — tile models onto grid

and the command "help tile" will show the tile documentation that says the default spacing is 1.3.  So to make closer spacing you could use

tile spacing 0.8.

The optimal spacing unfortunately depends on the shapes of your models because the models have different extents along different axes.

Tom

On Nov 22, 2022, at 9:02 AM, Hassan, Sergio (NIH/NIAID) [E] via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Hello,
I recently requested via Phil Cruz the 'tile' command, which I learned it was recently introduced. I have been using it successfully. However, there are two points I would like to bring to your attention (I asked Phil to ask you, but not sure he reached out)

1) when a session is saved as .cxs and I quit the program, after opening it again, the most important feature of the 'tile' command (rotations around each own axis) is lost. The tile distribution is still there, but now the entire thing rotates around a common axis. I need to apply 'tile' again to make it work, but this resets all the modifications I made in the saved session (these modifications include those in point 2 below).

2) any chance to add an argument to the 'tile' command so that the default spatial distribution, which assigns a 'distance' between near neighbors, can be adjusted with, say, 'zoom in" or "zoom out" or crowd in/out? I noticed the default puts each panel too far away from its neighbors for my taste, so I need to "move" them to make them look closer to one another.

thanks
s
_____________________________________
Sergio A. Hassan
https://bioinformatics.niaid.nih.gov/cmm/
BCBB/NIAID/NIH/DHHS
301 761 7221 (office) 301 741 5579 (mobile)

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