[Chimera-users] [External] Re: Combine focuse refined maps in Chimera

[Zheng, Fengwei]

Dear Elaine,

Thanks a bunch for your kind and detailed explanation!
I aligned those two focus refined maps to my consensus map first, and also resampled them on the grid of it. Actually, the difference I noticed is very slightly, thus can be omitted, I just a little worry that whether I used the correct command. Have a wonderful night!

Best,
Fengwei



________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, May 3, 2021 16:48
To: Zheng, Fengwei <Fengwei.Zheng at vai.org>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: [External] Re: [Chimera-users] Combine focuse refined maps in Chimera

Dear Fengwei,
Thanks for the compliments!

As I understand it, the only difference when you change the order of the input maps in the "vop maximumum"  command is if their grids are different (i.e. not exactly the same number of grid points in exactly the same locations) because by default (no "onGrid" map specified) the grid of the first one is used for the output map, and the second map is resampled to those points, which causes some loss in its resolution (more explanation in link below).  In that case, you need to decide which grid you want and then order them accordingly.

It sounds like you might want to use "vop add" instead of "vop maximum" but I suppose the results could be the same if the two densities do not overlap at all.

vop add
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add>
vop maximum
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#maximum>

loss in resolution from resampling
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On May 3, 2021, at 1:31 PM, Zheng, Fengwei <Fengwei.Zheng at vai.org> wrote:
>
> Dear Chimera developers:
>
> Thank you so much for developing this powerful and elegant software for our community!
>
> I am a newbie in cryoEM, and recently I got a consensus map, and split it into two parts to do the further focused refinement, after that I want to combine them together, and then to build my model.
>
> I learned that the command "vop maximum #0 #1" can achieve this, what I did is that, firstly, I used this command to merge my consensus map with one focused map, and then merged the resulted map with my second focused map, but it seems that the order of those two maps in my executable command (e.g. #0 #1 or #1 #0) will lead to slightly different resulting map~ I just wondering if this is the correct way to combine my focused maps, or there are other commands can achieve this better?
>
> Appreciate!
>
> Best,
> Fengwei
>
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