[Chimera-users] Fitting and measuring lengths in volume data

Tom Goddard goddard at cgl.ucsf.edu
Fri Mar 2 10:49:59 PST 2007

Hi Mazdak,

  To fit a PDB model in a map in Chimera you can hand place the model in 
roughly the right location and then do a computational optimization that 
maximizes the density at the atom positions.  Here are instructions:


Your map grid plane spacing has to be set correctly in Angstroms since 
the PDB model coordinates are in Angstroms.  Adjust the map grid plane 
spacing using the volume dialog menu entry Features / Origin and Scale 
and change the Voxel Size entry fields and press the Enter key to use 
those new values.  Voxel size is the same as grid plane spacing.

  You can measure the length between two markers.  Just select the link 
(ctrl click on it with the left mouse button) and use keyboard shortcut 
"pl".  You first have to turn on keyboard shortcuts using menu entry 
Tools / General Controls / Accelerators On.  Here are more details


For more info on volume data capabilities look at the Guide to Volume 
Data Display


I will look at map merging today if I have time.  So far I have been 
busy all week.


Mazdak Radjainia wrote:
> Hi Tom,
> There are actually two more tasks where I was hoping that chimera could help
> me.
> 1. I would like to fit high resolution data from a coordinate file in a
> low-electron density map. Can chimera perform such a docking/fitting? I
> tried to do it manually but I couldn't resize the opened pdb file towards my
> .mrc electron density map.
> 2. Is it possible to measure the length of a link between two markers? I
> tried to use the experimental "distance to surface" feature. But it never
> measures the distance between two markers which I hoped it could do.
> I really appreciate that you are already helping me out with map-merging
> feature which I hope doesn't cause too much trouble. It's just great to know
> if I could do the entire molecular visualization and structure analysis in
> chimera?  
> Cheers
> Mazdak

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