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<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">“close session<o:p></o:p></p>
<p class="MsoNormal">preset inter<o:p></o:p></p>
<p class="MsoNormal">light default<o:p></o:p></p>
<p class="MsoNormal">log clearâ€<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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: ‘<span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">this is equivalent to re-starting the program without having to actually do so</span>’<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Moritz<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Date: </b>Friday, August 5, 2022 at 15:23<br>
<b>To: </b>Tom Goddard <goddard@sonic.net><br>
<b>Cc: </b>Hunkeler, Moritz <Moritz_Hunkeler@DFCI.HARVARD.EDU>, chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>, Moritz, Michelle <Michelle.Moritz@ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] maps not on same grid in new ChimeraX?<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"> External Email - Use Caution
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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?<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
<br>
<br>
> On Aug 5, 2022, at 12:19 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Moritz,<br>
> <br>
> 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.
<a href="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">
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</a><br>
> <br>
> I've also made a feature request for the reset command. <a href="https://secure-web.cisco.com/1_7Q2UY4mlUUAh0jcexDMgCUTF7OrTWtRxNDbvRZNuDqFJg09eAc-u-laNqhWcRnAeADlJBUl1Re5L3Zj15ybMsy0ieIexOzdWjgFsqYk_t51gxn8mWfgU0umpidp0dh3otOW7pxazvh176fTQAxagDerg4SKwg4e272u4-ok3llrRPPEbssQNPAvlAizwfBrFjRmwY92JWFck1E6nX1ItxBLiQhDRtQo-1fS0O8awynCnrfGKPyyjgi4AdJV8PMPVkwfOhFnq1jFdgGLnFjMCJVDZdcs_PSpW1pE2Lir343rXCXHTTlGVx1sP6HdqMt0B73YMQTCJHstK0kdayjmDw/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7406">
https://secure-web.cisco.com/1_7Q2UY4mlUUAh0jcexDMgCUTF7OrTWtRxNDbvRZNuDqFJg09eAc-u-laNqhWcRnAeADlJBUl1Re5L3Zj15ybMsy0ieIexOzdWjgFsqYk_t51gxn8mWfgU0umpidp0dh3otOW7pxazvh176fTQAxagDerg4SKwg4e272u4-ok3llrRPPEbssQNPAvlAizwfBrFjRmwY92JWFck1E6nX1ItxBLiQhDRtQo-1fS0O8awynCnrfGKPyyjgi4AdJV8PMPVkwfOhFnq1jFdgGLnFjMCJVDZdcs_PSpW1pE2Lir343rXCXHTTlGVx1sP6HdqMt0B73YMQTCJHstK0kdayjmDw/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7406</a><br>
> <br>
> Thanks for suggesting these improvements!<br>
> <br>
> Tom<br>
> <br>
> <br>
>> On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
>> <br>
>> Hi,<br>
>> <br>
>> 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.<br>
>> <br>
>> 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).<br>
>> <br>
>> Best,<br>
>> Moritz<br>
>> <br>
>> From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
>> Date: Thursday, August 4, 2022 at 14:54<br>
>> To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
>> Subject: [chimerax-users] maps not on same grid in new ChimeraX?<br>
>> <br>
>> Hello, I recently updated my ChimeraX to version1.<span style="font-family:"Segoe UI Symbol",sans-serif">â </span>4(2022-06-03).<span style="font-family:"Segoe UI Symbol",sans-serif">â </span> 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.<span style="font-family:"Segoe UI Symbol",sans-serif">â </span> As I recall, in previous versions of Chimera,
<br>
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>> <br>
>> Hello,<br>
>> 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?<br>
>> Thanks for your help,<br>
>> Michelle<br>
>> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at
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