[chimerax-users] maps not on same grid in new ChimeraX?

Fri Aug 5 12:38:20 PDT 2022

Hi, ‘close session’ does not reset everything to the same state as you have when opening a new instance of chimeraX. E.g. tile, background color, lighting choice, silhouette choice and I think also depth cue settings (not sure here) all stay as they were before closing the session. And I am sure there are other settings that stay when closing a session.

This can become a problem when using scripts to make figures and some settings from the first script (let’s say you used flat lighting) is kept for when running the second script (even though you wanted default lighting.

Of course it’s possible to circumvent these problems with closing chimeraX every time before running a new script, or starting every script with something like

“close session
preset inter
light default
log clear”

But for convenience I would prefer if the close session button actually resets to default (or if there was a ‘reset’ button/command that would revert everything back to default). For example, in pyMOL there is the command ‘reinitialize’. From their wiki: ‘this is equivalent to re-starting the program without having to actually do so’

Best,
Moritz

ps: When playing around just now I think that e.g. lighting actually gets reset if the first new model file you open is a PDB, but not if it’s map. I wonder whether that is the intended behavior?

From: Elaine Meng <meng at cgl.ucsf.edu>
Date: Friday, August 5, 2022 at 15:23
To: Tom Goddard <goddard at sonic.net>
Cc: Hunkeler, Moritz <Moritz_Hunkeler at DFCI.HARVARD.EDU>, chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>, Moritz, Michelle <Michelle.Moritz at ucsf.edu>
Subject: Re: [chimerax-users] maps not on same grid in new ChimeraX?
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As far as I knew, "close session" is supposed to do this, so you wouldn't necessarily need a "reset" command.  Or maybe "reset" would do it without closing any of your data, is that the intention?
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 5, 2022, at 12:19 PM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Moritz,
>
>   I see, using the tile command sets the rotation mouse mode to rotate each displayed model about its own center.  And when you close those models to open new data it stays in that mode which is confusing.  I agree that closing the original models you tiled should change the rotation mouse mode back to rotating about a common center point.  I've made a bug report to fix that.  https://secure-web.cisco.com/1oyIHZGvEMg4UTMuUo6OrUkXWN-iXt8IRo2P55D1A5Og6QHSVtVbZ-RfwUbT-QJE2YGq_xbF0w3vdGDXFPv8rtmHwBxj_KCe2H1J_kbJNjQBfDqLMg57m2ls9LQx-zg2N62OrIg0FElEJOQ64KnaYmFNfTVk9EVcRdgXjjrlSBDsH6pWkBpvIYs0YTI0ATFYmHWBDJLYACaDtkux_F47DYT1iRxbMJoM-blsEMhuKudePDU1tL8uTW0FPHY8Cqai4D10oHHKGoargBSzDnb_7N2RwestrGx0SpNbFAwqpIv79LL0kbO5OYMnVBEhwEov3IRnqZq4q9zb2oKGEPMy2cA/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7405
>
>   I've also made a feature request for the reset command. https://secure-web.cisco.com/1_7Q2UY4mlUUAh0jcexDMgCUTF7OrTWtRxNDbvRZNuDqFJg09eAc-u-laNqhWcRnAeADlJBUl1Re5L3Zj15ybMsy0ieIexOzdWjgFsqYk_t51gxn8mWfgU0umpidp0dh3otOW7pxazvh176fTQAxagDerg4SKwg4e272u4-ok3llrRPPEbssQNPAvlAizwfBrFjRmwY92JWFck1E6nX1ItxBLiQhDRtQo-1fS0O8awynCnrfGKPyyjgi4AdJV8PMPVkwfOhFnq1jFdgGLnFjMCJVDZdcs_PSpW1pE2Lir343rXCXHTTlGVx1sP6HdqMt0B73YMQTCJHstK0kdayjmDw/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7406
>
>   Thanks for suggesting these improvements!
>
>        Tom
>
>
>> On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Hi,
>>
>> not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session.
>>
>> Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc).
>>
>> Best,
>> Moritz
>>
>> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
>> Date: Thursday, August 4, 2022 at 14:54
>> To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
>> Subject: [chimerax-users] maps not on same grid in new ChimeraX?
>>
>> Hello, I recently updated my ChimeraX to version1.⁠4(2022-06-03).⁠ It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size.⁠ As I recall, in previous versions of Chimera,
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>> Hello,
>> I recently updated my ChimeraX to version1.4(2022-06-03).  It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size.  As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated.  Is there a preference that I need to set in the latest version in order for this to happen?
>> Thanks for your help,
>> Michelle
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