[Chimera-users] Finding dimensions of density map

[Elaine Meng]

If I’d known of another way I would have told you!   The other way is to use python, as we said, but any details of that are beyond my skill set.

Elaine


> On Jul 12, 2019, at 1:02 PM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> 
> Hi Elaine,
>  
> One if fine. But is there a way to do it without the GUI? The method you suggest required me to hand select the corners. I am writing a Python program so I am using --nogui.
>  
> Best,
> Ryan Harlich
>  
> Sent from Mail for Windows 10
>  
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, July 12, 2019 9:22:38 AM
> To: Ryan Harlich
> Cc: chimera-users at cgl.ucsf.edu BB
> Subject: Re: [Chimera-users] Finding dimensions of density map
>  
> Hi Ryan,
> I think I did understood you: My suggestion to save the volume outline box as a molecule would give you 8 atoms at the corners, in PDB format.  However, there is no similar thing to get a collective bounding box for multiple datasets.  You’d just have to get a box for each volume data set and then figure out for yourself the min and max in each dimension among all the boxes.  As Tom G said, if this is something you want to do repeatedly, python scripting may be the only reasonable approach.
> Elaine
> 
> > On Jul 11, 2019, at 4:05 PM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> > 
> > I tried doing what you suggested and not sure how voxel size and origin will give you the bounding box. The other suggestion I am not sure if you understood what I am trying to accomplish or I did not understand what you were suggesting.
> >  
> > I am basically trying to get the bounding box. I tried with one atom and its bounding box would be small so what I did cut my volume. So I thought instead of one atom I can get eight atoms in all corners so when I resample it does not cut any of my volume because of the bounding box. I also want the biggest bounding box of two volumes.
> >  
> > Best,
> > Ryan Harlich
> >  
> > Sent from Mail for Windows 10
> >  
> > From: Ryan Harlich
> > Sent: Thursday, July 11, 2019 1:29:22 PM
> > To: chimera-users at cgl.ucsf.edu BB
> > Subject: RE: [Chimera-users] Finding dimensions of density map
> >  
> > Hi Elaine,
> >  
> > I am doing it no GUI via command line so I cannot select with mouse.
> >  
> > Thanks,
> > Ryan Harlich
> >  
> > Sent from Mail for Windows 10
> >  
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Thursday, July 11, 2019 12:49:19 PM
> > To: Ryan Harlich
> > Cc: 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.
> > 
> > <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=qLa0zvb7%2F9qeEOWFk%2BZfEJHi%2FBAhyCPi07BJf0LuRRA%3D&reserved=0>
> > <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=fxqKjEiOqwrZJAlgyvOXl8iJrLQ0Juc8o2ZiVLVgP98%3D&reserved=0>
> > 
> > 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
> > 
> > <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fmeshmol.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641027366&sdata=LAs5XM%2BXu%2BOGFXKxu7Z5MwqXkmMZPZe9GhBfLCBn2WA%3D&reserved=0>
> > 
> > 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> 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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