[Chimera-users] Selecting one ID 0 when two ID 0s are present

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 9 09:20:32 PDT 2019

Hi Ryan,
You did mention that overall purpose briefly, but not why you clicked those specific buttons in Volume Viewer.  If I understand your goals correctly, clicking those buttons (or equivalent commands) shouldn’t be in your workflow anyway.

There is no “solid surface” only the mutually exclusive display styles “solid” (cloudlike) or “surface” (isosurface).  Those two are just display settings, and so is zoning in the Volume Viewer dialog, which simply hides part of the density map without actually erasing it.  None of those change the density map.

If you just use “surface” style (which I suppose could be called a solid surface, as opposed to mesh) then the solid model won’t exist.  When “solid” style is used, both models are listed, even though only the solid one is shown, but I don’t see any reason why you would need to use solid style. Commands to set display style are in the previous message, but probably the default style when you first open the map is surface anyway so you may not need any command.

To zone and then save the zoned version of the map I believe there are two equivalent approaches:

(1) “vop zone” to create a new map followed by “volume” command “save” option to save it to file

- OR -

(2) “sop zone” (command equivalent of zone feature in Volume Viewer GUI) followed by  “volume” command “save” option with “maskZone true"

… however, if you already used the “volume” command “save” on your masked map, it should have saved just the zone since maskZone is true by default. But maybe you used a save dialog (GUI) instead, which doesn’t expose all those saving options.

Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 8, 2019, at 3:39 PM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> Hi Elaine,
> Oh I thought I said what I was trying to do. I am try take a map that has solid and surface. I also have a pdb structure. I want to get the chain on the pdb structure. Invert and delete the invert. Now I only have the chain desired. I know how to do that part with command line. Now that part I am having trouble with is zoning the map that has both solid and surface and save. I am able to zone it no problem, but when I save and reopen it is not what I zoned. So overall I am trying to get only the chunk of the density map for the selected chain of the pdb structure.
> Best,
> Ryan Harlich
> Sent from Mail for Windows 10
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Thursday, August 8, 2019 3:32:59 PM
> To: Ryan Harlich <ryanharlich at hotmail.com>
> Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Selecting one ID 0 when two ID 0s are present
> Sorry, e-mailed prematurely by accidentally clicking send.  Continuing to reply below
> > On Aug 8, 2019, at 3:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 
> > Hi Ryan,
> > I don’t understand the description of what you’re doing in the GUI.  I don’t think there is anything in the Volume Viewer GUI that selects a model.  There are One and All buttons that are only shown if you used Features… Planes, and they don’t have anything to do with selection.  If I choose “surface” display style and then click “All” nothing happens because that is only relevant to “solid” display style.  If you click “One” then it changes to “solid” display style, which creates another model with the same number.  Switching to “surface” again would get rid of the solid model.
> > 
> > When you are showing solid style
> …. two models are listed in Model Panel with the same number because they are just alternative displays of the same density map.  
> > 
> > Switching to 
> ….”surface” style again gets rid of the solid model.  I’m not sure why the surface model stays around when the solid style is shown; it may be to keep track of the positions of the thresholds (the isosurface levels).
> You can control which style is shown with the “volume” command, e.g. 
> volume all style solid
> volume all style surface
> There is still only one density map, however, so you may just be able to use that model number in commands even though it’s listed twice in the Model Panel when solid style is shown.  You didn’t say what you were trying to do with that model number, however…  or, you could just get rid of it by showing surface style.
> > 
> > 
> > Best,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> >> On Aug 8, 2019, at 8:42 AM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> >> 
> >> Hi Chimera,
> >> 
> >> I have a problem where there are two ID 0. One is the normal density map the other is a solid (or what seems to be a movie of the protein). I want to select the density map. In the GUI interface I would open volume viewer and select radio button surface for category Style. Then a little below select All instead of One. I was wondering how to do this with command line?
> >> 
> >> What I am trying to do is get a chain of the pdb structure and zone the density map. However the files are really big so I am trying to do it via ssh on another computer so I will be doing it with the –nogui flag. So if I can do everything via command line that would be great.
> >> 
> >> Best,
> >> Ryan Harlich

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