Hi I was trying to use the volume eraser to remove density outside of a sphere on my em map. When I enabled keyboard shortcuts and then used the shortcut command eo what I got back was an identical copy to the original, i.e. no erasure. If I used es then everything in the circle was erased as expected. Am I missing something? CheersJohn John M. Flanagan PhD. Professor Department of Biochemistry and Molecular Biology Penn St. College of Medicine Milton Hershey Medical Center Hershey PA, 17033
Hi John, this tends to work reliably normally, but sometimes it happens you trick yourself into thinking it's not working, usually when you have multiple densities loaded. Make sure that you: 1) have the right density active when you do the erasing 2) don't have other overlapping densities visible (typically a copy of the same density, since the erasing procedure generates a copy it works on rather than working on the loaded original) Since they are identical, you wouldn't notice that your erased volume has changed. Best J ________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of JOHN FLANAGAN <jmf27@psu.edu> Sent: Thursday, March 21, 2019 1:04 PM To: UCSF Chimera Mailing List Subject: [Chimera-users] (no subject) Hi I was trying to use the volume eraser to remove density outside of a sphere on my em map. When I enabled keyboard shortcuts and then used the shortcut command eo what I got back was an identical copy to the original, i.e. no erasure. If I used es then everything in the circle was erased as expected. Am I missing something? Cheers John John M. Flanagan PhD. Professor Department of Biochemistry and Molecular Biology Penn St. College of Medicine Milton Hershey Medical Center Hershey PA, 17033
Hi John, I could not reproduce your problem: I opened a map, started Volume Eraser and moved the sphere, and then used command “ac eo” and it erased the density outside of the sphere. (The “ac” command allows using shortcuts without switching into that mode, but otherwise should be the same as using “eo” by itself when you are in shortcut mode.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ac.html> Otherwise I can only suggest to doublecheck what Juraj suggests. You can see which map models are present and show/hide them with the Model Panel (open from Favorites menu), and the “active” or “current” map is the one with name highlighted in the Volume Viewer dialog. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.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 Mar 21, 2019, at 7:02 AM, Ahel,Juraj <juraj.ahel@imp.ac.at> wrote:
Hi John,
this tends to work reliably normally, but sometimes it happens you trick yourself into thinking it's not working, usually when you have multiple densities loaded. Make sure that you:
1) have the right density active when you do the erasing 2) don't have other overlapping densities visible (typically a copy of the same density, since the erasing procedure generates a copy it works on rather than working on the loaded original) Since they are identical, you wouldn't notice that your erased volume has changed.
Best
J From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of JOHN FLANAGAN <jmf27@psu.edu> Sent: Thursday, March 21, 2019 1:04 PM To: UCSF Chimera Mailing List Subject: [Chimera-users] (no subject)
Hi I was trying to use the volume eraser to remove density outside of a sphere on my em map. When I enabled keyboard shortcuts and then used the shortcut command eo what I got back was an identical copy to the original, i.e. no erasure. If I used es then everything in the circle was erased as expected. Am I missing something?
Cheers John
John M. Flanagan PhD. Professor Department of Biochemistry and Molecular Biology Penn St. College of Medicine Milton Hershey Medical Center Hershey PA, 17033
Thanks, I think that I figured it out. CheersJohn On Thu, Mar 21, 2019 01:48 PM, "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> wrote:
Hi John,
I could not reproduce your problem: I opened a map, started Volume Eraser and moved the sphere, and then used command “ac eo” and it erased the density outside of the sphere. (The “ac” command allows using shortcuts without switching into that mode, but otherwise should be the same as using “eo” by itself when you are in shortcut mode.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ac.html>
Otherwise I can only suggest to doublecheck what Juraj suggests. You can see which map models are present and show/hide them with the Model Panel (open from Favorites menu), and the “active” or “current” map is the one with name highlighted in the Volume Viewer dialog. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.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 Mar 21, 2019, at 7:02 AM, Ahel,Juraj <juraj.ahel@imp.ac.at> wrote:
Hi John,
this tends to work reliably normally, but sometimes it happens you trick yourself into thinking it's not working, usually when you have multiple densities loaded. Make sure that you:
1) have the right density active when you do the erasing 2) don't have other overlapping densities visible (typically a copy of the same density, since the erasing procedure generates a copy it works on rather than working on the loaded original) Since they are identical, you wouldn't notice that your erased volume has changed.
Best
J From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of JOHN FLANAGAN <jmf27@psu.edu> Sent: Thursday, March 21, 2019 1:04 PM To: UCSF Chimera Mailing List Subject: [Chimera-users] (no subject)
Hi I was trying to use the volume eraser to remove density outside of a sphere on my em map. When I enabled keyboard shortcuts and then used the shortcut command eo what I got back was an identical copy to the original, i.e. no erasure. If I used es then everything in the circle was erased as expected. Am I missing something?
Cheers John
John M. Flanagan PhD. Professor Department of Biochemistry and Molecular Biology Penn St. College of Medicine Milton Hershey Medical Center Hershey PA, 17033
John M. Flanagan PhD. Professor Department of Biochemistry and Molecular Biology Penn St. College of Medicine Milton Hershey Medical Center Hershey PA, 17033
participants (3)
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Ahel,Juraj -
Elaine Meng -
JOHN FLANAGAN