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Hernando J Sosa

14 Jul 2020 14 Jul '20

11:05 a.m.

Dear Chimera, I there a chimera command equivalent to Features -> subregion selection -> crop in the Volume viewer menu? Thanks Hernando

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Elaine Meng

14 Jul 14 Jul

11:54 a.m.

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. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimension... 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: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accel... The shortcuts themselves: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist... You can use accelerators directly as commands with the "ac" command, for example to use the "eb" shortcut, command: ac eb http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ac.html 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 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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Hernando J Sosa

12:28 p.m.

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 Sent: Tuesday, July 14, 2020 2:54 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB 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.uc... 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.uc... The shortcuts themselves: https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.uc... 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.uc... 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 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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Elaine Meng

12:48 p.m.

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: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#zone ... or if you want to make a new map that has zero values outside the zone, the "vop zone" command: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone 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. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover 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 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 Sent: Tuesday, July 14, 2020 2:54 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB 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.uc...

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.uc... The shortcuts themselves: https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.uc...

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.uc...

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 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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Hernando J Sosa

15 Jul 15 Jul

1:26 p.m.

Hi Elaine, Is there a command equivalent to VolumeViewer->File->Duplicate? Thks H. ________________________________ From: Elaine Meng Sent: Tuesday, July 14, 2020 3:48 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB 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, 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.uc... ... 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.uc... 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.uc... 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 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 Sent: Tuesday, July 14, 2020 2:54 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB 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.uc...

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.uc... The shortcuts themselves: https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.uc...

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.uc...

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 wrote:

Dear Chimera, I there a chimera command equivalent to Features -> subregion selection -> crop in the Volume viewer menu? Thanks Hernando

Reply

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Elaine Meng

1:50 p.m.

New subject: command to duplicate map

Hi Hernando, Seems like you can do it by adding a map to nothing else with "vop add" ... for example to make a copy of map #1 as new map #2 vop add #1 model #2 http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add Whether it is really EXACTLY the same as duplication using the Volume Viewer File menu in all situations, I do not know. Elaine

On Jul 15, 2020, at 1:26 PM, Hernando J Sosa wrote:

Hi Elaine, Is there a command equivalent to VolumeViewer->File->Duplicate? Thks H.

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Tom Goddard

2:23 p.m.

New subject: command to duplicate map

Yes, volume add is the standard trick to copy a map in Chimera. In ChimeraX it is the more obvious "volume copy #1". Tom

On Jul 15, 2020, at 1:50 PM, Elaine Meng wrote:

Hi Hernando, Seems like you can do it by adding a map to nothing else with "vop add" ... for example to make a copy of map #1 as new map #2

vop add #1 model #2

http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add

Whether it is really EXACTLY the same as duplication using the Volume Viewer File menu in all situations, I do not know.

Elaine

...
On Jul 15, 2020, at 1:26 PM, Hernando J Sosa wrote:

Hi Elaine, Is there a command equivalent to VolumeViewer->File->Duplicate? Thks H.

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Elaine Meng
Hernando J Sosa
Tom Goddard