[chimerax-users] [new-map-options] Error when using the "subregion" option

[Tom Goddard]

Hi Arthur,

  I fixed the bug, will be in tonight's ChimeraX builds.  The daily builds section is below the production releases on the ChimeraX download page:

	https://www.rbvi.ucsf.edu/chimerax/download.html#daily

  I interpreted command

	volume copy #1 subregion 150,150,150,300,300,300

which includes one grid point beyond the edge of the map of size 300 (indices from 0 to 299) as cropping to the part actually in the map.  An alternative would be to add zeros where you request a region outside the map bounds, but I think that is rarely desired so I did not do that.

	Tom


> On Nov 13, 2020, at 10:48 AM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Arthur,
> 
>   That is a bug and I will fix it, probably today.
> 
>   It is easy to avoid.  The map EMDB 22000 has grid size 300.  But ChimeraX (and Chimera) uses grid indices that start at 0, so the index range along each axis is 0-299, so the copy command
> 
> 	volume copy #1 subregion 150,150,150,300,300,300
> 
> is asking to include grid index 300 which is one beyond the edge of the map.  Still it should clamp it to 299.  But if you use the command
> 
> 	volume copy #1 subregion 150,150,150,299,299,299
> 
> it works correctly and gives a grid size 150 map as expected.
> 
> 	Tom
> 
> 
>> On Nov 13, 2020, at 10:14 AM, Arthur Ecoffet <arthurecoffet at gmail.com <mailto:arthurecoffet at gmail.com>> wrote:
>> 
>> Dear ChimeraX developers,
>> 
>> When using the "subregion" option for different map-related functions (volume morph, volume copy) I encountered the following error : 
>> ValueError: could not broadcast input array from shape (150,150,150) into shape (151,151,151)
>> 
>> File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\map\volume.py", line 982, in writable_copy
>> g.array[:,:,:] = self.region_matrix(r)
>> 
>> If you want to reproduce the error, I worked on EMDB22000 and I typed in the console : 
>> volume copy #1 subregion 150,150,150,300,300,300 
>> alternatively 
>> volume morph #1 #2  subregion 150,150,150,300,300,300  raises the same error. 
>> 
>> I tried on two versions of ChimeraX (including the last stable from September) and got the same error twice. 
>> Would you have any idea how to solve this? 
>> 
>> Thanks very much, 
>> Best,
>> Arthur 
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