[Chimera-users] local cross-correlation coefficient

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 8 08:42:22 PDT 2014


Hi Zhihai Li,
Why not just use the single correlation value reported by Fit in Map?  That makes more sense to me than trying to get local values and then averaging them back together, which would accumulate various interpolation and rounding errors.   I can't think of a convenient way to do the averaging, but even if I could, I wouldn't recommend it.
Elaine

On Jul 8, 2014, at 12:29 AM, 李智海 <21620101152414 at stu.xmu.edu.cn> wrote:

> Hi Elaine, 
> Thanks for your quick reply! The “vop localCorrelation” command is great for representing the different local correlation value between two maps.
> Here I have a further question. I want to get an exact local correlation value to show how the atomic model fit the density map. Can Chimera output the mean local correlation value between the input maps?
> Thanks!
> Zhihai Li
> 
> School of Life Sciences, Xiamen University.
> Xiang'an Road(South), Xiang'an District, Xiamen City,
> Fujian Province, China. 361102
> 
> 在 2014年7月8日,上午12:33,Elaine Meng <meng at cgl.ucsf.edu> 写道:
> 
>> Hi Zhihai Li,
>> The correlation from Fit in Map is defined here:
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html#correlation>
>> 
>> This is a single value calculated for the whole fit, not a local correlation that would have different values in different places.  The correlation is calculated from two maps.  If you were fitting an atomic structure into a map, a map was simulated from the atomic structure and then compared with the other map.
>> 
>> For *local* correlation between two maps, see command "vop localCorrelation":
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#localCorrelation>
>> 
>> This vop command would create a third map containing the local correlation values between your two input maps.  Then you could color the isosurface of one of the input maps to show the different local correlation values in different places, for example with Surface Color (in menu under Tools… Volume Data).
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
>> 
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> On Jul 6, 2014, at 10:30 PM, 李智海 <21620101152414 at stu.xmu.edu.cn> wrote:
>> 
>>> Hi,
>>> I performed tool "Fit in map” to calculate the correlation value, i was wondering whether the value is the same as local cross-correlation coefficient (local CCC).
>>> Thanks in advance for your help!
>>> Best wishes for you!
>>> Zhihai Li
>>> 
> 
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