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
Dear Yocheved, I think you would have to cut off the X,Y data using Region min,max so that the size is 108,108,108. As far as I know, Chimera doesn't have a feature to add grid points with zero values to make the Z dimension larger, which would allow creating a cube without losing X,Y data. Although there is a "vop boxes" command to extract cubic boxes, it does not extend beyond the current data. Although there is a "vop cover" command to extend a map, it assumes periodicity (wraps the data around instead of adding zeroes), which does not sound like what you want. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 3, 2011, at 2:31 AM, יוכבד wrote:
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
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.... Tom
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
participants (3)
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Elaine Meng -
Tom Goddard -
יוכבד