[Chimera-users] Save multiple fitted maps in Chimera

[Elaine Meng]

Thanks for mentioning "vop add," since I forgot to include it!   It does the adding and resampling all at once.

ChimeraX and Chimera both have this command, although in ChimeraX it is documented as "volume add":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add>

Elaine

> On Dec 13, 2021, at 1:25 PM, Huabin Zhou <Huabin.Zhou at UTSouthwestern.edu> wrote:
> 
> 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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