Chimera-dev December 2015

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chimera-dev@cgl.ucsf.edu

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match API change
by Eric Pettersen 21 Dec '15

21 Dec '15

Just a heads up that as a side effect of now reporting both the full and pruned RMSD of an iterated match, the number of return values from Midas.match(), Midas.matchXform(), and MatchMaker.match() changed. The first two added the full RMSD just after the pruned RMSD in their tuple of return values, and the latter did a similar thing, though it returns a list of such (now larger) tuples. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimera-dev] Save the map after hide dust
by Tom Goddard 08 Dec '15

08 Dec '15

Hi Gary, I made it a bit easier to invert the shown portion of the map surface by adding an "sop invertShown" command. It will be in tonight's daily build. So to mask the dust on map #0 you could use sop hideDust #0 size 25 sop invertShown #0 mask #0 #0 invert true Would be nice to make this easier -- maybe in our next generation Chimera. Tom > On Dec 8, 2015, at 6:35 PM, Tom Goddard wrote: > > Hi Gary, > > Good to hear from you. The hide dust feature does not change the density map, it only hides the small connected surface pieces. You could set the map grid points to zero inside the dust blobs with the mask command. But first you need to be able to show only the dust and there is no command to do that. I've attached a Python script that does that. You select the map surface (ctrl-click) that you have done hide dust on, then open the surfinvert.py script to show only the dust. Then use the mask command > > mask #0 sel invert true > > to mask the density map (#0) to the selected surface (dust blobs only shown) and invert, since you want to keep everything outside the dust blobs, not everything inside the dust blobs. I tried it, works. But if you lower the threshold on the new map then of course you see more dust. > > Tom > > <surfinvert.py> > > The surfinvert.py script is also on the Chimera Python scripts page > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > > >> On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote: >> >> Hi Tom, >> >> I like the density map after hide density map, is there any way to save the >> density map after dust hide? Every time I save the density map, it saved the >> original map instead of density map after hidden dust. >> >> Thanks a lot >> Gary >> >> >> >> >

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