Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus
Hi Yangqi, Yes, see command “vop subtract”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract> Keep in mind that if the two aren’t on the same grid, there may be small differences due to the need to sample them at the same points to do the subtractions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2018, at 4:39 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi
Hi Elaine, Thank you for your response! I tried using the command and I have been trying two maps which looks very similar, but with different resolution (3.6 A (yellow) vs 3.2 A (grey)) and with different pixel size (1.05 vs 0.822). Will this affect the gridding? (I am not very familiar with what you mean by the same grid). Best, Yangqi Sent from Mail for Windows 10 From: Elaine Meng Sent: Friday, November 16, 2018 7:45 PM To: Yangqi Gu Cc: chimera-users Subject: Re: [Chimera-users] Difference map Hi Yangqi, Yes, see command “vop subtract”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract> Keep in mind that if the two aren’t on the same grid, there may be small differences due to the need to sample them at the same points to do the subtractions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2018, at 4:39 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi
Hi Yangqi, The grid is where the points with values are in space. If the points are spaced differently (different voxel size.), then the grids are different. They are also different if the spacing is the same but the location or offset is different. Best, Elaine
On Nov 17, 2018, at 2:40 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Hi Elaine, Thank you for your response! I tried using the command and I have been trying two maps which looks very similar, but with different resolution (3.6 A (yellow) vs 3.2 A (grey)) and with different pixel size (1.05 vs 0.822). Will this affect the gridding? (I am not very familiar with what you mean by the same grid). Best, Yangqi
Sent from Mail for Windows 10
From: Elaine Meng Sent: Friday, November 16, 2018 7:45 PM To: Yangqi Gu Cc: chimera-users Subject: Re: [Chimera-users] Difference map
Hi Yangqi, Yes, see command “vop subtract”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Keep in mind that if the two aren’t on the same grid, there may be small differences due to the need to sample them at the same points to do the subtractions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2018, at 4:39 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I see. So the pixel size should not matter as long as they are normalized to the same voxel size? About the offset, do you mean the origin of the map? Like origin coordinates? Best, Yangqi Sent from Mail for Windows 10 From: Elaine Meng Sent: Sunday, November 18, 2018 12:56 PM To: BuddySphinx Cc: chimera Subject: Re: [Chimera-users] Difference map Hi Yangqi, The grid is where the points with values are in space. If the points are spaced differently (different voxel size.), then the grids are different. They are also different if the spacing is the same but the location or offset is different. Best, Elaine
On Nov 17, 2018, at 2:40 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Hi Elaine, Thank you for your response! I tried using the command and I have been trying two maps which looks very similar, but with different resolution (3.6 A (yellow) vs 3.2 A (grey)) and with different pixel size (1.05 vs 0.822). Will this affect the gridding? (I am not very familiar with what you mean by the same grid). Best, Yangqi
Sent from Mail for Windows 10
From: Elaine Meng Sent: Friday, November 16, 2018 7:45 PM To: Yangqi Gu Cc: chimera-users Subject: Re: [Chimera-users] Difference map
Hi Yangqi, Yes, see command “vop subtract”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Keep in mind that if the two aren’t on the same grid, there may be small differences due to the need to sample them at the same points to do the subtractions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2018, at 4:39 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Each map is a rectangular box with values at points. I have no idea what you mean by “pixel." Either the boxes are in exactly the same places with the points at the same places or they are not. I think you do not need to worry about this too much because you have no choice: you already have two maps you want to subtract. I was only trying to say that interpolation of values may introduce some small loss of resolution, which is already described in the “vop subtract” documentation for which I sent a link earlier. Elaine
On Nov 18, 2018, at 10:13 AM, BuddySphinx <yangqi.gu@yale.edu> wrote:
I see. So the pixel size should not matter as long as they are normalized to the same voxel size? About the offset, do you mean the origin of the map? Like origin coordinates? Best, Yangqi
Sent from Mail for Windows 10
From: Elaine Meng Sent: Sunday, November 18, 2018 12:56 PM To: BuddySphinx Cc: chimera Subject: Re: [Chimera-users] Difference map
Hi Yangqi, The grid is where the points with values are in space. If the points are spaced differently (different voxel size.), then the grids are different. They are also different if the spacing is the same but the location or offset is different. Best, Elaine
On Nov 17, 2018, at 2:40 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Hi Elaine, Thank you for your response! I tried using the command and I have been trying two maps which looks very similar, but with different resolution (3.6 A (yellow) vs 3.2 A (grey)) and with different pixel size (1.05 vs 0.822). Will this affect the gridding? (I am not very familiar with what you mean by the same grid). Best, Yangqi
Sent from Mail for Windows 10
From: Elaine Meng Sent: Friday, November 16, 2018 7:45 PM To: Yangqi Gu Cc: chimera-users Subject: Re: [Chimera-users] Difference map
Hi Yangqi, Yes, see command “vop subtract”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Keep in mind that if the two aren’t on the same grid, there may be small differences due to the need to sample them at the same points to do the subtractions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2018, at 4:39 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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BuddySphinx -
Elaine Meng -
Yangqi Gu