Re: [scipion-users] Comparing 2 volume maps

[Estrella F. G. <me....@cn...>]

Hi Dmitry,

I usually use xmipp3 - align volume with "local" search strategy, and it 
works fine for me in this kind of comparison workflow. To use local 
strategy the volumes must be close enough. I haven't use fast Fourier 
method nor exhaustive, but the help of the protocol says: "... Be aware 
that the Fast Fourier algorithm requires a special compilationof Xmipp 
(--cltomo flag)...", maybe that is the cause why it is not working 
properly. However, I can not tell you so much about xmipp3 - align 
volume, maybe someone from Xmipp with more experience can say something 
else.

Regards,

Estrella FG

On 12/10/21 10:32, Dmitry Semchonok wrote:
> 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... <mailto: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... <mailto: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
>>
>>
>>
>>
>>
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