[Chimera-users] Save the map after hide dust

[Tom Goddard]

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



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
> 
> 
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/813fd64c/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: surfinvert.py
Type: text/x-python-script
Size: 473 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/813fd64c/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/813fd64c/attachment-0001.html>