[chimerax-users] volume onesmask usage question

[Tom Goddard]

Hi Alexis,

  The volume onesmask command only takes a surface.  You may pass it a volume but it only sees it as a surface, so it knows nothing about the volume grid.  So the current volume onesmask cannot do what you want.  I guess it might need a new option onGrid where you specify you want the onesmask on the grid of a specified volume.  I'll take a look to see how hard it would be to add that.

	Tom


> On Dec 11, 2019, at 10:15 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Alexis,
> The “remaining options” referred to those which are shown in the usage line for “volume onesmask” but not explained directly in that section:
> 
> • volume onesmask  surface-spec  [ border  B ] [ spacing  S | Sx,Sy,Sz ] [ pad  distance ] [ extend  N ] [ slab  width | d1,d2 ] [ invertMask  true | false ] [ axis  vector-spec ] [ sandwich  true | false ] [ fillOverlap  true | false ] [ modelId  M ]
> 
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask>
> 
> Options not shown in that usage line are not available, at least as far as I knew when I wrote the documentation.  You can always check with the “usage” command, e.g. “usage volume onesmask”  will show all of its current options in the Log.
> 
> The differences are that mask has a fullmap option whereas onesmask has border and spacing options. I don’t know the rationale for the differences, sorry.  I imagine you might be able to get the result you wanted with a combination of operations, maybe using “volume mask” first and then “volume threshold” to reset all nonzero values to 1, but I don’t know how well that would work, and it seems unnecessarily indirect.  If I think of anything better, will let you know.  
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Dec 11, 2019, at 9:58 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
>> 
>> Hi there,
>> 
>> I was trying to use "volume onesmask" to go quickly from a dusted surface of a low-pass-filtered volume to a mask volume with the same dimensions, spacing, etc. as the input map. 
>> 
>> I thought "fullmap" might be a way to achieve this (the doc says "The remaining options are the same as described for volume mask"), but I don't think that option actually works with "volume onesmask":
>> 
>> volume onesmask #3 fullmap true
>> Expected a keyword
>> 
>> Is there a "onesmask"-like operation or set of options that creates an output volume that's on the same grid as the input volume?
>> 
>> Thanks,
>> Alexis
> 
> 
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