Help Generating a Volume to use for 2D classification template generation
Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh Joshua M. Denson PhD Candidate (Johnson Group) Dept. of Chemistry and Biochemistry Utah State University
Hi Josh, Our map expert may be away this week, but I'll try to answer this. There is no way to directly specify a cube in the "molmap" command. It does have an "onGrid" option to generate the map on the grid of another map. So one possibility might be to make a blank map with "volume new" with the desired "size" and "gridSpacing" values and then use that zero-valued map with the "onGrid" option of "molmap." The tricky part might be making the zero-valued map go in the right place, but maybe it would work to just make it first and then move the structure inside of it rougtly at the center after showing its (the map's) outline box. volume new <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> molmap <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.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 Feb 21, 2023, at 1:14 PM, Joshua Denson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh
This should work I think. To get the model centered on the box, you can first center on the new map, then use the "cofr model" argument of "move" to move the molmap model to the center of rotation before resampling on the new grid. Cheers Oli
On Feb 21, 2023, at 1:51 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Josh, Our map expert may be away this week, but I'll try to answer this.
There is no way to directly specify a cube in the "molmap" command. It does have an "onGrid" option to generate the map on the grid of another map. So one possibility might be to make a blank map with "volume new" with the desired "size" and "gridSpacing" values and then use that zero-valued map with the "onGrid" option of "molmap." The tricky part might be making the zero-valued map go in the right place, but maybe it would work to just make it first and then move the structure inside of it rougtly at the center after showing its (the map's) outline box.
volume new <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new>
molmap <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.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 Feb 21, 2023, at 1:14 PM, Joshua Denson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
It worked thanks for your help! Best Josh Joshua M. Denson PhD Candidate (Johnson Group) Dept. of Chemistry and Biochemistry Utah State University From: Oliver Clarke<mailto:olibclarke@gmail.com> Sent: Tuesday, February 21, 2023 4:43 PM To: ChimeraX Users Help<mailto:chimerax-users@cgl.ucsf.edu>; Elaine Meng<mailto:meng@cgl.ucsf.edu> Cc: Joshua Denson<mailto:joshua.denson@usu.edu> Subject: Re: [chimerax-users] Help Generating a Volume to use for 2D classification template generation This should work I think. To get the model centered on the box, you can first center on the new map, then use the "cofr model" argument of "move" to move the molmap model to the center of rotation before resampling on the new grid. Cheers Oli
On Feb 21, 2023, at 1:51 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Josh, Our map expert may be away this week, but I'll try to answer this.
There is no way to directly specify a cube in the "molmap" command. It does have an "onGrid" option to generate the map on the grid of another map. So one possibility might be to make a blank map with "volume new" with the desired "size" and "gridSpacing" values and then use that zero-valued map with the "onGrid" option of "molmap." The tricky part might be making the zero-valued map go in the right place, but maybe it would work to just make it first and then move the structure inside of it rougtly at the center after showing its (the map's) outline box.
volume new <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new>
molmap <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.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 Feb 21, 2023, at 1:14 PM, Joshua Denson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Josh, I made a ChimeraX feature request to add a molmap option to allow you to specify the grid size. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8542 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8542#ticket> May be able to add that in a week or two when I am back from vacation. Tom
On Feb 21, 2023, at 1:14 PM, Joshua Denson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5.
Best Josh
Joshua M. Denson PhD Candidate (Johnson Group) Dept. of Chemistry and Biochemistry Utah State University
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Elaine Meng -
Joshua Denson -
Oliver Clarke -
Tom Goddard