Re: [Chimera-users] Cannot resample to voxel size of 1
It sounds like you just want to resample a map at a new grid spacing. Chimera does not have such a feature. The vop resample command is intended make the grids of two different maps match each other. Tom
On Jul 22, 2019, at 1:54 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Tom,
I need the voxel size to be 1, so subdivideSurface and subdivisionLevel options won’t work. Also, vop new won’t work because I need it to have the same bounding box as the input surface.
Best, Ryan Harlich
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From: Tom Goddard <goddard@sonic.net> Sent: Monday, July 22, 2019 1:49:38 PM To: Ryan Harlich <ryanharlich@hotmail.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Cannot resample to voxel size of 1
Hi Ryan,
Resampling only works on the grid of another map as you can see from the documentation so "vop new" allows you to make that map. If you just want to make the mesh of a surface depiction of a map finer then look at the volume command subdivideSurface and subdivisionLevel options.
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23dispsurf&data=02%7C01%7C%7C470a6f16006d4c0c583208d70ee61f25%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994253835707622&sdata=X%2BgN1OYI3XC%2FfvqO6CxIAK4%2F7Mr94hAZg8LSjxVcgj4%3D&reserved=0>
Tom
On Jul 22, 2019, at 12:03 PM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
Hi Elaine,
I think you missed the point. I am trying to take an existing surface and resample it to a grid Spacing of 1. I am not sure I see the point of making a new map.
Best, Ryan Harlich
From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Monday, July 22, 2019 11:59:06 AM To: Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Cannot resample to voxel size of 1
Hi Ryan, You can make a new map of whatever grid spacing you want without any atoms using “vop new”: <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvop.html%23new&data=02%7C01%7C%7C0fae3f40d7504ce6f8a908d70ed6ac3d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994187477432851&sdata=pVKM4r3k6C%2Bd%2FNBnpxZOR8qwzr5Q6dUeqFXLvHkEwqE%3D&reserved=0 <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvop.html%23new&data=02%7C01%7C%7C470a6f16006d4c0c583208d70ee61f25%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994253835727638&sdata=iGSe0Ft5vnC0N%2Bx7EOcwhwFhyMQPERz6bWMvQsosACo%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 22, 2019, at 11:33 AM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
Hi Chimera Bug Team,
I am unable to resample surface to a grid spacing of 1 to be 1 voxel.
Currently I do this: 'molmap #2 6 gridSpacing 1\n' 'vop resample #3 onGrid #2.1\n'
But this requires me to have a pdb structure. I would like to do this without a pdb structure.
Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z.
Any help would be much appreciated. Option 1 would be a much better approach.
Best, Ryan Harlich
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Tom Goddard