[Chimera-users] Map's Box size

Tom Goddard goddard at sonic.net
Mon Apr 4 09:34:18 PDT 2011

Hi Yocheved,

   Creative use of the "vop add" command in Chimera can extend your 
volume box in the z direction.  Here's the trick:

     open your map (#0)
     vop add #0
     move z 300 model #1 coord #1
     vop add #1
     move z -300 model #2 coord #2
     vop add #0,1,2 scale 1,0,0

Here's what this does.  Each "vop add #0" command makes a copy of your 
map -- usually vop add is used to add two or more maps, but if you just 
give it one map it will make a copy.  Then the "move" command move the 
two map copies along the map z axis by 300 Angstroms.  That's how much z 
extension I'll get at the top and bottom of the map.  Then the last 
command adds my original map and these two new maps but uses scaling 
factors zero for the two map copies (just adds zeros).  The vop add 
command automatically creates a new map on the same grid as the first 
argument (#0) extended to cover the other maps.  You can trim this map 
to exactly the cube size you need with volume dialog Features / Region 
Bounds, and save it with volume dialog File / Save Map As....


> Hi
> Can I please get your help with map resizing.
> I have a map with a box size 250,269,108. To run a map fitting script 
> I need the map to have a cubic size.
> Using the volume viewer- Region min max step x - I was able to play 
> with the box size the problem is I can't get the entire map into a 
> cubic box (Z axis is to small).
> Is there a way to enlarge the box on the Z axis?
> Thank you
> Yocheved

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