Re: [scipion-users] Comparing 2 volume maps

[Dmitry S. <Sem...@gm...>]

Hi Estrella, 

I followed your suggestions for the volumes comparison. 
But the xmipp-alignment doesn’t seem to do the good job for me. I used the fast Fourier method (the default one was standby for the indefinite time somehow). 

I downloaded and overlapped the refenence map and output of xmipp-alignment map in Chimera. 
So next I did Fit in model - the aligned map moved nicely to the position.


Do you have any clue why?



Thank you.

Sincerely,
Dmitry











> On 8. Oct 2021, at 08:50, Estrella Fernández Giménez <me....@cn...> wrote:
> 
> Hello Dmitry,
> 
> I suggest you to use some of the new programs in Xmipp (and of course integrated in the correspondant Scipion plugin), which are actually implemented for this kind of task.
> The programs are:
> 
> xmipp3 - volumes adjust: it allows you to have the volumes in the same numerical frame, thus, you can compare there in a reliable way (same threshold).
> 
> xmipp3 - volumes subtraction: it performs the alignment described above and then it computes the subtraction between the volumes, thus, it result should be the differences between the volumes.
> 
> xmipp3 - volume consensus: applying first "volume adjust protocol" described above, then this protocol is able to make a fusion of a set of volumes, taking the best parts of each one. The result will be a volume consensus between the input. The result is automatically displayed in chimera with a colormap that indicates you the degree of similarity among the input maps (what we call a "difference map").
> 
> You can find more details of these protocols in this paper: https://www.sciencedirect.com/science/article/pii/S104784772100085X?via%3Dihub
> 
> This three protocols have to be applied once the set of volumes has the same box size and pixel size (you can use xmipp3 - crop/resize protocol to achive this). Also, the volumes have to be properly aligned (using xmipp3 - align volume, for example).
> 
> Feel free to contact me in case you have any doubt. Hope it helps!
> 
> Regards,
> Estrella FG
> 
> 
> Dmitry Semchonok <Sem...@gm...> escribió:
> 
>> <>Dear colleagues,
>> 
>> 
>> 
>> My task is to compare 2 volume maps to see the differences. The maps are biologically pretty similar.
>> 
>> What strategy shall I undergo and tool to select?
>> 
>> 
>> 
>> Apart from biological similarities they are different for the pixel size, box size, resolution and volume threshold.
>> 
>> 
>> 
>> Thank you
>> 
>> 
>> 
>> Sincerely,
>> 
>> <>
>> Dmitry
> 
> 
> 
> 
> 
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users