[Chimera-users] Volume save after volume changes

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 1 15:41:28 PDT 2019

Hi Ryan,
Maybe you are actually trying to mask the map with the surface, i.e. delete parts of the map that are inside (or outside) some surface.  If so, see command “volume mask.”  In general the “volume operations” are commands that actually edit the map, creating a modified copy.

Volume operations including masking:

I hope this helps,

> On Jul 1, 2019, at 3:34 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ryan,
> These are all isosurface display changes.  The map consists of density values at points on a 3D grid.  A map can be shown with multiple isosurfaces, or no isosurfaces at all.  None of the map values are changing.
> Elaine
>> On Jul 1, 2019, at 1:07 PM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
>> Hi Elaine,
>> What about hideDust? I was trying to resample a selected surface that had hide dust alterations to it. Would this also only be a display setting too then; therefore, I could not hide dust then resample. That is what I am trying to accomplish, but the alteration does not seem to save.
>> Best,
>> Ryan Harlich
>> Sent from my Verizon, Samsung Galaxy smartphone
>> -------- Original message --------
>> From: Elaine Meng <meng at cgl.ucsf.edu> 
>> Date: 7/1/19 12:58 PM (GMT-08:00)
>> To: Ryan Harlich <ryanharlich at hotmail.com> 
>> Cc: chimera-users at cgl.ucsf.edu
>> Subject: Re: [Chimera-users] Volume save after volume changes
>> Hi Ryan,
>> Changing the isosurface contour level is not changing the map.  It’s analogous to opening an atomic structure from the PDB and then changing its coloring…. just a display setting, not an alteration of the underlying data, and these display settings aren’t part of the formats in which the data are saved.
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>> On Jul 1, 2019, at 9:04 AM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
>>> Hi Chimera,
>>> I am having problems saving changes of volume.
>>> Here is my script:
>>>       • open C:\Users\ Desktop\density.map
>>>       • volume #0 level 1.0
>>>       • sel #0
>>>       • volume sel save C:\Users\ Desktop\density2.mrc
>>> This does not save the change at line 2. How can I go about to save the change?
>>> Best,
>>> Ryan Harlich

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