[Chimera-users] Finding dimensions of density map

[Elaine Meng]

Hi Ryan,
The meshmol command creates a new atomic model from the mesh surface of the volume (map) model.  That is the whole purpose of the meshmol command.  You save the new atomic model (or its selected part) as a PDB file.
Elaine

> On Jul 16, 2019, at 1:39 PM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> 
> The help button is greyed out. Meshmol is an mrc and you said I could save it as a pdb. I don’t think this is possible. I did what you said.
>  
> Sent from Mail for Windows 10
>  
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, July 16, 2019 12:40:07 PM
> To: Ryan Harlich
> Cc: chimera-users at cgl.ucsf.edu BB
> Subject: Re: [Chimera-users] Finding dimensions of density map
>  
> Hi Ryan,
> You did not say what you did.  If using the save PDB dialog, you have to choose the model in the dialog as well as the selected-only option if you’ve used the mouse to select only the box part of the model in the window.
> 
> Click Help on dialogs when you are using them and you get an error, before asking on the list.
> Best,
> Elaine
> 
> > On Jul 16, 2019, at 11:55 AM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> > 
> > Hi Elaine,
> >  
> > I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected.
> >  
> > Best,
> > 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://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=mBl1i29nupLseHehVLHIZXq6s9bOIbolpz7vN3O06Pg%3D&reserved=0>
> > <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=KjazTdLtJitxTNVADDbu2guA6DoBP%2BuZG7Wxgrc7G%2B4%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://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fmeshmol.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=EdHtA6SACMhpm7nj5lyXWZPa3J77BNOoKEG8QjLVLqc%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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