[Chimera-users] Cannot resample to voxel size of 1

[Tom Goddard]

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 at 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
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>  
> From: Tom Goddard <goddard at sonic.net>
> Sent: Monday, July 22, 2019 1:49:38 PM
> To: Ryan Harlich <ryanharlich at hotmail.com>
> Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at 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 at hotmail.com <mailto:ryanharlich at 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
>>  
>> Sent from Mail <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986&data=02%7C01%7C%7C470a6f16006d4c0c583208d70ee61f25%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994253835717633&sdata=sKPYQqECuYa940LKtImp%2FevWeT%2BPg4iRNqUAmBSG1NQ%3D&reserved=0> for Windows 10
>>  
>> From: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
>> Sent: Monday, July 22, 2019 11:59:06 AM
>> To: Ryan Harlich <ryanharlich at hotmail.com <mailto:ryanharlich at hotmail.com>>
>> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB <chimera-users at cgl.ucsf.edu <mailto:chimera-users at 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 at hotmail.com <mailto:ryanharlich at 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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