[Chimera-users] crop map command

[Hernando J Sosa]

Thanks Elaine this would work. Another question assuming that I want to display a region of the map around a particular  structure of a model fitted into the map. What would be the formula o convert from  the  model atomic coordinates to the map grid coordinates?

thanks again

H.


________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, July 14, 2020 2:54 PM
To: Hernando J Sosa <hernando.sosa at einsteinmed.org>
Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] crop map command

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Hi Hernando,
With the "region" option of "volume" you can specify the subregion directly, e.g.

volume #2 region 13,4,0,22,25,29

... but in that case you would need to know the grid indices you want; it does not use the hand-drawn box.
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvolume.html%23dimensions&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4c9c4a35ed76471c52ad08d828276897%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303497009341013&sdata=vuBJRTAooDbFBZ2uHeNzeFi%2FSNCML6vgdxB2wJRVfjQ%3D&reserved=0>

However, you can give different cropped subregions different names ahead of time with the "volume" command "nameRegion" option,  and then switch between them in the display by name using this "region" option.  These options are explained in the link above.

I thought there might be a keyboard shortcut for it, but I don't see one.  I only see a keyboard shortcut "eb" to erase the map inside the box.

Chimera keyboard shortcuts tool:
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Faccelerators%2Faccelerators.html&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4c9c4a35ed76471c52ad08d828276897%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303497009341013&sdata=DiK%2FzcWg%2Bp35WJuAmMb2tOZmbycTQ2f4b%2FGDA2fdxVQ%3D&reserved=0>
The shortcuts themselves:
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Faccelerators%2Falist.html%23voledit&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4c9c4a35ed76471c52ad08d828276897%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303497009341013&sdata=zQlDa7U%2BV%2Ba3lDuKtUkSF63BK0VBgiOLqEjNiTOA%2FsA%3D&reserved=0>

You can use accelerators directly as commands with the "ac" command, for example to use the "eb" shortcut, command:

ac eb

<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fac.html&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4c9c4a35ed76471c52ad08d828276897%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303497009341013&sdata=5j6pU3npPJDch2TB6xLguGVn5ng5XBLEG%2BaFsj6oiYY%3D&reserved=0>

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

> On Jul 14, 2020, at 11:05 AM, Hernando J Sosa <hernando.sosa at einsteinmed.org> wrote:
>
> Dear Chimera,
> I there a chimera command equivalent to Features -> subregion selection -> crop in the Volume viewer menu?
> Thanks
> Hernando

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