[Chimera-users] generating a map from a atomic model with the same size of its reference map

Tom Goddard goddard at sonic.net
Tue Apr 14 10:28:52 PDT 2015

Hi Zhihai,

  If you want the map computed from an atomic model but on a grid that matches a reference map then you should compute the map with molmap and then resample it on the reference map grid.  If #0 is the atomic model and #1 the reference map.

	molmap #0 8 edgePadding 50
	vop resample #0 onGrid #1

Here the 8 is the resolution for the computed map and 50 Angstroms controls how far beyond the molecule bounding to compute the map.


> On Apr 13, 2015, at 9:00 PM, 李智海  wrote:
> hi,
> here I want to generate a density map from a atomic model in Chimera,  then convert the generating map into .pif file to do as the initial map performing in Auto3dem.
> I have met some questions to successfully finish these work.
> 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size.
> 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. 
> Thanks in advanced!
> Best wishes!
> Zhihai Li
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