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Dear Elaine,</div>
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Thank you so much for your quick reply. The ChimeraX is much faster than Chimera. With vol resample, I was able to get the new individual map on fitted positions. </div>
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BTW, for any other user's future reference, Clara Altomare pointed out the following command could add multiple density map together: vop add #1-99</div>
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Thanks,</div>
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Huabin</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 13 December 2021 14:23<br>
<b>To:</b> Chimera <chimera-users@cgl.ucsf.edu>; Huabin Zhou <Huabin.Zhou@UTSouthwestern.edu><br>
<b>Subject:</b> Re: [Chimera-users] Save multiple fitted maps in Chimera</font>
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<div class="PlainText">EXTERNAL MAIL<br>
<br>
If you use ChimeraX instead (which has the same fitting capabilities), saving a ChimeraX session has an option to include density maps in the file. However, it sounds like that might be an extremely huge file, perhaps impractically large.<br>
<br>
In general, however, ChimeraX is much better/faster for working with large data than Chimera.<br>
<br>
ChimeraX sessions:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session">https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session</a>><br>
<br>
ChimeraX homepage, download quick link is on the left<br>
<<a href="https://www.rbvi.ucsf.edu/chimerax/index.html">https://www.rbvi.ucsf.edu/chimerax/index.html</a>><br>
<br>
Elaine<br>
<br>
> On Dec 13, 2021, at 12:14 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
><br>
> Dear Huabin,<br>
> You could save a Chimera session, but you'd also need to keep the input tomogram files and density map files in their current locations since the session file does not include them.<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sessions.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sessions.html</a>><br>
><br>
> For saving multiple maps to one file, I believe the only choice is "Chimera map format"<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output</a>><br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#chimap">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#chimap</a>><br>
><br>
> HOWEVER, as I understand it, simply saving a map to a file does not preserve any rotations and translations of that map such as from fitting. So first you may need to resample each density map to create a new density map in the new orientation, as discussed
here:<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting</a>><br>
><br>
> I hope this helps,<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>
>> On Dec 13, 2021, at 11:59 AM, Huabin Zhou via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
>><br>
>> Dear Chimera team and users,<br>
>> I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative
orientations of the individual models?<br>
>> Thank you!<br>
>> Best,<br>
>> Huabin<br>
><br>
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