[Chimera-users] Extracting masked map region using selected sop piece?

Oliver Clarke olibclarke at gmail.com
Thu Apr 9 07:44:28 PDT 2015

Hi all,

I find the sop command (particularly 'sop split' and 'sop hideDust metric volume rank') to be very useful for viewing a molecular envelope at a low threshold in an otherwise noisy map.

I would like to save the volume enclosed by a single sop piece as a separate volume, but it does not seem like this is possible - when I select a sop piece and use 'volume nameregion’ to assign it a name, and then attempt to write just that region to an mrc, it saves the whole map. Is there some way to do this that I am missing?

I realize that a similar outcome can be achieved with segger, but for larger maps this can be very slow (and potentially involve multiple cycles of selection and regrouping), whereas sop operations are almost instantaneous, so I feel it would be a valuable adjunct capability to that offered by segger.

Also, the behaviour of sop split seems a little counterintuitive to me. When I use 'sop split' on a volume, it generates a new model with a different ID for the split map - fine so far. However, the original map seems to be completely invisible - it is listed as displayed in the model panel, but if I undisplay the split map in the model panel and toggle display of the original map in the model panel, nothing happens. If I go to the volume viewer, the original map is listed as displayed, and if I toggle it off and then on again there, it reappears. It seems like it would be maybe simpler for the user to just automatically undisplay the original map upon creation of the sop split map, but not to prevent the user from redisplaying it in the model panel. Here is a link to a screen recording demonstrating what I mean: https://www.dropbox.com/s/g40u9dhj0xslcbf/sop_split.mov?dl=0 <https://www.dropbox.com/s/g40u9dhj0xslcbf/sop_split.mov?dl=0>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150409/b54053b8/attachment.html>

More information about the Chimera-users mailing list