[chimerax-users] volume onesmask usage question

[Tom Goddard]

Hi Alexis,

  I added an onGrid option to the volume onesmask command.  So you can create a mask from the volume #1 surface on the grid of volume #1 using

	volume onesmask #1 ongrid #1

This will be in tonight's ChimeraX builds.

	Tom


> On Dec 11, 2019, at 10:20 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> 
> Thanks Elaine,
> 
> Thanks for the clarification - I figured I wasn't reading things carefully enough. 
> 
> I worked with "volume mask" followed by "volume threshold" exactly as you suggest, and it worked fine. 
> 
> The "volume onesmask" as it is now stands out from most other volume operations in that it creates an entirely new grid and doesn't even let us stay on the same grid as the input. This makes it not-very-useful for my regular work, but I'm sure there was a good reason initially.
> 
> Just saw Tom's email re. surface v volume distinction. Makes sense of course, though I do think harmonizing the options across volume operations would be nice if easily achievable. 
> 
> Cheers,
> Alexis
> 
> On Wed, Dec 11, 2019 at 10:15 AM Elaine Meng <meng at cgl.ucsf.edu <mailto: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 <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 <mailto: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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