[Chimera-users] How to crop a map

Tom Goddard goddard at sonic.net
Wed Jun 24 11:30:58 PDT 2015


You can crop a map using volume dialog menu Features / Region Bounds, then save it with volume dialog File / Save Map As….  Other Chimera map capabilities are described in the Guide to Volume Data Display in Chimera:

	http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html <http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>

  Tom


> On Jun 23, 2015, at 7:52 PM, 李智海  wrote:
> 
> Adding to the previous one.
> the map I want to convert has a same pixel size with the data set. So maybe the question could be that how can I cutting the boundaries of the map to fit the size of reconstruction images. 
> 
> Thanks!
> 
> Zhihai Li
> 
> 
>> On Jun 24, 2015, at 10:44 AM, 李智海  wrote:
>> 
>> Hi, Tom
>> An another question, 
>> I want to make a reference map for reconstruction, here I have a map but with different map size from my raw image, how can I scale the map dimensions into a specific value without changing the centre coordinates.
>> Thanks!
>> 
>> Zhihai Li
>> 
>> 
>>> On Jun 24, 2015, at 2:00 AM, Tom Goddard  wrote:
>>> 
>>> If you used the Chimera Segment Map dialog (volume dialog menu Tools / Segment Map) then you select a segment (ctrl click on it) and use Segment Map menu entry Regions / Mean and SD.  If you segmented the map by some other means and have the pieces as separate maps use volume dialog menu Tools / Measure Mean, SD, RMS.
>>> 
>>> 	Tom
>>> 
>>> 
>>>> On Jun 23, 2015, at 6:42 AM, 李智海  wrote:
>>>> 
>>>> Hi,
>>>> Here I want to evaluate the flexibility of variable domains of a density map. How can I quantify the mean intensity of segmented parts by Chimera? Thanks!
>>>> 
>>>> Best wishes!
>>>> 
>>>> Zhihai Li
>>>> 
>>>> Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics.
>>>> School of Life Sciences, Xiamen University.
>>>> Xiang'an Road(South), Xiang'an District, Xiamen City,
>>>> Fujian Province, China.
>>>> 
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>>>> Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
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>>> 
>> 
> 

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