<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Arthur,<div class=""><br class=""></div><div class=""> 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:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/download.html#daily" class="">https://www.rbvi.ucsf.edu/chimerax/download.html#daily</a><br class=""><div><br class=""></div><div> I interpreted command</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>volume copy #1 subregion 150,150,150,300,300,300</div><div><br class=""></div><div>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.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 13, 2020, at 10:48 AM, Tom Goddard <goddard@sonic.net> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Arthur,<div class=""><br class=""></div><div class=""> That is a bug and I will fix it, probably today.</div><div class=""><br class=""></div><div class=""> 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</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume copy #1 subregion 150,150,150,300,300,300</div><div class=""><br class=""></div><div class="">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</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume copy #1 subregion 150,150,150,299,299,299</div><div class=""><br class=""></div><div class="">it works correctly and gives a grid size 150 map as expected.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Nov 13, 2020, at 10:14 AM, Arthur Ecoffet <<a href="mailto:arthurecoffet@gmail.com" class="">arthurecoffet@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear ChimeraX developers,<div class=""><br class=""></div><div class="">When using the "subregion" option for different map-related functions (volume morph, volume copy) I encountered the following error : <br class=""><div style="margin: 0px; white-space: pre-wrap;" class=""><i class="">ValueError: could not broadcast input array from shape (150,150,150) into shape (151,151,151)<br class=""><br class="">File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\map\volume.py", line 982, in writable_copy<br class=""></i>g.array<i class="">[:,:,:] = self.region_matrix(r)
</i>If you want to reproduce the error, I worked on EMDB22000 and I typed in the console :
<i class="">volume copy #1 subregion 150,150,150,300,300,300
</i>alternatively
<i class="">volume morph #1 #2 subregion 150,150,150,300,300,300 </i> raises the same error. </div><div style="margin: 0px; white-space: pre-wrap;" class=""><br class=""></div><div style="margin: 0px; white-space: pre-wrap;" class="">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, </div><div style="margin: 0px; white-space: pre-wrap;" class="">Best,</div><div style="margin: 0px; white-space: pre-wrap;" class="">Arthur </div></div></div>
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