[chimera-dev] Save the map after hide dust

[Gang (Gary) Ren]

Hi Tom,

Wow.. that will be awesome!! I can't wait to use this new operation. The
operation in Chimera is so cool, we love it.

Best regards

Gary

 

From: Tom Goddard [mailto:goddard at sonic.net] 
Sent: Tuesday, December 08, 2015 6:53 PM
To: chimera-dev at cgl.ucsf.edu
Cc: Xiaobo Zhai; Gang (Gary) Ren
Subject: Re: Save the map after hide dust

 

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

 

 

 

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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