[Chimera-users] Save multiple fitted maps in Chimera

[Huabin Zhou]

Dear Elaine,

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.

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


Thanks,

Huabin




________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 13 December 2021 14:23
To: Chimera <chimera-users at cgl.ucsf.edu>; Huabin Zhou <Huabin.Zhou at UTSouthwestern.edu>
Subject: Re: [Chimera-users] Save multiple fitted maps in Chimera

EXTERNAL MAIL

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.

In general, however, ChimeraX is much better/faster for working with large data than Chimera.

ChimeraX sessions:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session>

ChimeraX homepage, download quick link is on the left
<https://www.rbvi.ucsf.edu/chimerax/index.html>

Elaine

> On Dec 13, 2021, at 12:14 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Dear Huabin,
> 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.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sessions.html>
>
> For saving multiple maps to one file, I believe the only choice is "Chimera map format"
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#chimap>
>
> 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:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Dec 13, 2021, at 11:59 AM, Huabin Zhou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>
>> Dear Chimera team and users,
>> 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?
>> Thank you!
>> Best,
>> Huabin
>
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