[Chimera-users] Finding dimensions of density map

Tom Goddard goddard at sonic.net
Thu Jul 11 16:09:06 PDT 2019

Chimera does not have any command to make bounding boxes from fake atoms.  If you want to do something this far beyond the scope of normal Chimera uses then you will have to program in Python.  There is a little documentation on how to write Python programs that use Chimera capabilities that you can find by searching online.  If you are new to this it will probably take you several weeks of effort to learn how to draw a simple box -- so I don't recommend pursuing that unless you are very interested.


> On Jul 11, 2019, at 1:29 PM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> Hi Elaine,
> I am doing it no GUI via command line so I cannot select with mouse.
> Thanks,
> Ryan Harlich
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
> From: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> Sent: Thursday, July 11, 2019 12:49:19 PM
> To: Ryan Harlich
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Finding dimensions of density map
> Hi Ryan,
> The “Coordinates” section of Volume Viewer (open from its Features  menu) gives values used to convert between the dataset grid and Cartesian coordinates.  You’d have to back-calculate from the origin index and voxel size.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>>
> Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model.  That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file.  E.g. if the volume model is #4, command:
> meshmol #4 1
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>>
> then,
> … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box
> ...use “write” command or File… Save PDB with their respective option to save only the selected part
> I hope this helps,
> Chimera  ;-)
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich at hotmail.com <mailto:ryanharlich at hotmail.com>> wrote:
> > 
> > Hi Chimera,
> >  
> > I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
> >  
> > Best,
> > Ryan Harlich
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