[Chimera-users] generate raised cosine smoothed mask with "mask ones" and "vop falloff"

Tom Goddard goddard at sonic.net
Mon Nov 25 12:25:00 PST 2013

Hi Dieter,

  You should be able to generate a smooth volume mask using "mask ones" and "vop falloff" in Chimera.  Here's an example making a smooth cylinder mask

	shape cylinder radius 100 height 100 caps true
	mask ones #0 border 10
	vop falloff #1 iter 100

The boundary smoothing "vop falloff" is described on this web page


Maybe you saw that page and got tripped up because it gave the wrong option name "step" instead of "iterations" in the vop falloff command -- I've fixed the web page.


On Nov 24, 2013, at 12:41 AM, Dieter Blaas  wrote:

> Hi,
>    I was wondering whether it is possible to generate binary raised cosine smooth masks with 'masked ones' followed by 'vop falloff' or anything alike. I'd like to generate an arbitrary mask (from a volume) with a smooth transition (over some few pixels) to 0 but I did not really find adequate parameters. Is this possible?
> Thanks, D.
> -- 
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,

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