[Chimera-users] crop map command

[Hernando J Sosa]

Hi Elaine,

Is there a command equivalent to VolumeViewer->File->Duplicate?

Thks

H.

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, July 14, 2020 3:48 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,
I don't know such a formula, it would have to include the rotation and translation of one model relative to the other.

Normally to limit map isosurface display to the parts near some atoms, you would just use the "sop zone" command:
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fsop.html%23zone&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7Cfcde677321dc4ecee30e08d8282ef597%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303530044371189&sdata=6LZZuqF%2F3Ecjt%2FosUQmF2eJImZbf5Iei4LpGKqHJrnI%3D&reserved=0>

... or if you want to make a new map that has zero values outside the zone, the "vop zone" command:
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvop.html%23zone&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7Cfcde677321dc4ecee30e08d8282ef597%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303530044371189&sdata=5KLY0oWj7lV3q7yx8CsKDHov%2F5yqSC%2BPFmaQqiAmKpQ%3D&reserved=0>

Those would not give a rectangular box, however.

I can't think of a series of commands that would give you a rectangular box subregion of the original map on the bounding box of a molecule.  It would probably take python, and somebody else would have to advise on that.  Maybe "vop cover," but it sounds like it would only make a map bigger, not smaller, than its current size.
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvop.html%23cover&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7Cfcde677321dc4ecee30e08d8282ef597%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303530044371189&sdata=Q%2FFLm%2FZR5Pap00r8Oj%2B9mFa3guC3kdkSusqM0KVzHAs%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 12:28 PM, Hernando J Sosa <hernando.sosa at einsteinmed.org> wrote:
>
> 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
>
> CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.
>
> 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%7Cfcde677321dc4ecee30e08d8282ef597%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303530044371189&sdata=iyCmyf7XWu6JKwbBcZ4qv44Q8vKohHc9Ax3Ssl1PAOc%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%7Cfcde677321dc4ecee30e08d8282ef597%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303530044371189&sdata=eKIhzkh16aN64YeSjDEAvXgTG%2FDr8bYZNSBtucAWTWY%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%7Cfcde677321dc4ecee30e08d8282ef597%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303530044371189&sdata=K3PyzYXAjy3XZ6fyBPl%2FgRDybgkB3z4XVNY3hSTMfkw%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%7Cfcde677321dc4ecee30e08d8282ef597%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637303530044371189&sdata=Tp6GjeNKqn%2Fe5oKIJw4zM9QLlxDIVSflzagRbpQwhcA%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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