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

Tom Goddard goddard at sonic.net
Tue Nov 26 10:03:02 PST 2013


Hi Dieter,

  Chimera does not make masks with cosine falloff.  The only mask smoothing in Chimera is "vop falloff".  The algorithm is completely described in the Chimera manual (copied below) and basically amounts to a "heat equation" falloff -- the grid points outside the mask are assigned the average of the neighboring values, essentially the diffusion of heat from the masked ones region to the outside zeros region.  This works for any shape.

	Tom


"vop falloff volume-spec [ iterations M ] general-options

Smooth the boundaries of a masked map by replacing the value at each grid point outside the boundary with the average of the values of its six nearest neighbors, for M iterations (default 10). All grid points with values of zero before the first iteration are taken to be outside the boundary, thus assigned a new value at each iteration. Thanks to Greg Pintilie for the initial implementation."



Begin forwarded message:

> From: Dieter Blaas 
> Subject: Re: [Chimera-users] generate raised cosine smoothed mask with "mask ones" and "vop falloff"
> Date: November 26, 2013 8:34:17 AM PST
> To: Tom Goddard 
> 
> Hi Tom,
> 
>   thanks for these explanations! I am still not sure whether such a mask behaves like a mask made with e.g. xmipp_transform_mask or with spider MA SOFT.  I'd like to make an arbitrary mask (level 0 - 1) from a molecular volume which has a raised_cosine falloff. When comparing a spherical mask made with chimera (as given below) and with xmipp their histograms look quite different (probably also a question of the choice of parameters). The difference becomes much more striking when using a more irregular shaped molecular assembly. I found the Chimera procedure when looking for a method to make such masks as this is not provided in xmipp (only a sphere or a crown with raised-cosine but not an irregularly shaped mask). I want to use it in 3D-reconstructions......
> 
> Best, Dieter
> 
> 
> 
> 
>  
> 
> 
> Am 25.11.2013 21:25, schrieb Tom Goddard:
>> 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
>> 
>>  http://www.cgl.ucsf.edu/chimera/data/falloff-sep2012/falloff.html
>> 
>> 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.
>> 
>>  Tom
>> 
>> 
>> 
>> 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,
>> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> 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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