[Chimera-users] vop add

Tom Goddard goddard at sonic.net
Fri Jan 16 12:34:39 PST 2015


Hi Francisco,

  If you get an error, Chimera offers a Report a Bug button and you should use it.  I don’t know what your suggested new “vop merge” would do.  The idea I suggested of using thresholds to determine the boundary of maps and averaging only where they overlap is very poor as I described in my previous email.

	Tom


> On Jan 16, 2015, at 3:43 AM, Fco Javier Chichón  wrote:
> 
> Dear Tom
> 
> Thank you very much for your response.
> 
> We were trying to create the averaged volumes but most of the times we get an error message when using the scaleFactors options.
> 
> we used the combination of vop threshold, scale, multiply etc trying to create mask... it was unsuccessful, mainly due the errors.
> 
> At the end the less bad option was to use vop maximum. It will be better to average, but at least, it did not sum the intensities of the tomograms.
> 
> 
> It will be great to have a vop merge option if feasible. We will use this procedure very often, and chimera allow us to manually setup the volume fiting area and then, the fine positioning was generated perfectly with the volume-fit- tool.
> 
> 
> 
> 
> On 14/1/15 23:50, Tom Goddard wrote:
>> Hi Francisco,
>> 
>>   If you average two maps with “vop add #0,1 scale 0.5,0.5” then where the maps do not overlap the density value will be reduced by averaging when one map has a point inside the structure and one map has the point outside.  Another approach to “merging” would be to take the maximum of the two maps with "vop maximum”. If you really want to average the maps where both are greater than some threshold density, but where only one is greater than the threshold you simply use that map’s value then you will get discontinuities in the merged map at the boundary where both maps are above the threshold.  So I wouldn’t recommend that but it could be done with “vop threshold” to make a 0/1 mask for each map where it is above threshold, add those two masks to get the number of map values (0, 1 or 2 for each grid point) then divide the sum of the maps by that map.  Oops, there is no "vop divide”, only a “vop multiply”.  I don’t think you want to do that, but if you do let me know and I will add a vop divide to divide one map by another point-wise.
>> 
>> 	Tom
>> 
>> 
>>> On Jan 14, 2015, at 6:49 AM, Fco Javier Chichón wrote:
>>> 
>>> Dear all
>>> 
>>> I would like to merge several volumes.
>>> Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them.
>>> 
>>> Anyone know how to do that?
>>> 
>>> Thanks
>>> 
>>> -- 
>>> =======================================================
>>> Francisco Javier Chichón García
>>> 
>>> Centro.: Centro Nacional de Biotecnología
>>> Dept.: Macromolecular Structure
>>> Lab.: S1-S0.1
>>> Tel.: (+34) 91585-5497:4690
>>> =======================================================
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
> 
> -- 
> =======================================================
> Francisco Javier Chichón García
> 
> Centro.: Centro Nacional de Biotecnología
> Dept.: Macromolecular Structure
> Lab.: S1-S0.1
> Tel.: (+34) 91585-5497:4690
> =======================================================
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




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