[Chimera-users] Volume planes

Tue Feb 1 12:09:27 PST 2022

Hi Hernando,
As Tom said, fitting into a plane won't do anything, since it only uses the displayed subregion, which has to be 3-dimensional.

I believe that after the settings have been saved as preferences using the Features menu of the Volume Viewer dialog as I described in my first reply (which you would only do once), in later uses of Chimera they will apply to maps regardless of which method was used to open them. 

There are also corresponding options in the "volume" command, although I'm not sure whether they just apply to the current session or get saved in the preferences.  If using the GUI is not possible you could try those:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling>

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

> On Feb 1, 2022, at 11:59 AM, Hernando J Sosa via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thank you, Elaine, 
> 
> Another question: does the option to open/display the whole map would also work when using the open command to load the volume and without touching the Volume display dialogue? I am using a script to open and fit several coordinates models with minimal or no GUI use.
> 
> Also I did notice that if the map is opened/displayed as a single plane then the <fitmap> command does not work as intended.  It appears as is the model is fitted to an empty map. A workaround I found was to crop the map before fitting using the command <volume #map region ...>. The cropped map always seems to show all the planes (due to the smaller size?).
> 
> Best
> 
> Hernando.
> 
> 
> 
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, February 1, 2022 11:55 AM
> To: Hernando J Sosa <hernando.sosa at einsteinmed.edu>
> Cc: chimera-users at cgl.ucsf.edu List <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Volume planes
>  
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> 
> Dear Hernando,
> 
> (1) there is a setting for what size is shown as a plane.  In Volume Viewer menu, choose Features... Data Display Options. That shows more options in the Volume Viewer dialog.  In those options you can turn off (or change the size) for
> 
> "Show data when opened if smaller than [size] Mvoxels"
> "Show plane when data larger than [size] Mvoxels"
> 
> See data display options:
> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23disp-options&data=04%7C01%7Chernando.sosa%40einsteinmed.edu%7C64a1b9cb12ae413ea3e608d9e5a3ba90%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637793314824180790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=7DPQmSVlkp9h%2Fsf7XjLKwLeB896NzGU27QoNjUu3Xf0%3D&reserved=0>
> 
> Then you can save those settings in your preferences (so they will be used in the future) using Volume Viewer menu "Features... Save default dialog settings"
> 
> (2) for map-map fitting, the "fitmap" command has an "envelope" option of whether to use only the grid points in the fit map with values above the contour level in Volume Viewer. This option is default true but you can set it false to use all nonzero-valued grid points.  See fitmap options:
> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Ffitmap.html%23options&data=04%7C01%7Chernando.sosa%40einsteinmed.edu%7C64a1b9cb12ae413ea3e608d9e5a3ba90%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637793314824180790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qc7DeTt5awROTXhRTWPkDJ4JPYxTARpT1TBtnPpunh4%3D&reserved=0>
> 
> As far as I know, display step size does not affect the calculation.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Jan 31, 2022, at 6:48 PM, Hernando J Sosa via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera,
> >
> > I have a couple of questions:
> >       • When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size?
> >       • Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)?
> >
> > Thanks
> >
> > Hernando
> 
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