Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Next revision Both sides next revision
tutorial_energy_landscape [2017/06/23 09:32]
dhaselb 		tutorial_energy_landscape [2017/06/30 18:57]
kbertra2
Line 8: Line 8:
  
 Input for the analysis should be several 3D Volumes, that have the same size and are aligned on each other. To gain these we recomment the use of relion in combination with UCSF Chimera. Once a set of these 3D volumes is created they can be imported into the cow in one go by having them all in the same folder. ​ Input for the analysis should be several 3D Volumes, that have the same size and are aligned on each other. To gain these we recomment the use of relion in combination with UCSF Chimera. Once a set of these 3D volumes is created they can be imported into the cow in one go by having them all in the same folder. ​
- 
  
  
Line 26: Line 25:
 Additionally we will need the min and max values of the linear factors with respect to the chosen eigenimage. Those can be extracted using the the SQL logic with the following query: ​ Additionally we will need the min and max values of the linear factors with respect to the chosen eigenimage. Those can be extracted using the the SQL logic with the following query: ​
  
-     SELECT * FROM t0 WHERE linearFactorForEigenimage0 =(SELECT MIN(linearFactorForEigenimage0) from t0) +  ​SELECT * FROM t0 WHERE linearFactorForEigenimage0 =(SELECT MIN(linearFactorForEigenimage0) from t0) 
-     ​SELECT * FROM t0 WHERE linearFactorForEigenimage0 =(SELECT MAX(linearFactorForEigenimage0) from t0)+ 
 +  ​SELECT * FROM t0 WHERE linearFactorForEigenimage0 =(SELECT MAX(linearFactorForEigenimage0) from t0)
  
 For more convenience within the flow control we will append those two value carrying images ​ For more convenience within the flow control we will append those two value carrying images ​
  
 === Flow control ​ ===      === Flow control ​ ===     
 +
 +First we need too initialize two variables linearFactor and stepsize.  ​
 +
 +We will initialize the linearFactor as the minimal Value using a script
 + 
 +  cow.linearFactor = cow.io[0]["​linearFactorForEigenimage0"​]
 +
 +To visualize 10 intermediate structures we calculate the stepsize with a Calculate tool with 
 +
 +  cow.stepsize=(cow.io[1]["​linearFactorForEigenimage0"​]-cow.io[0]["​linearFactorForEigenimage0"​])/​10
 +  ​
 +We will use this calculation to trigger our first loop that should run for 10 iterations. The loop itself should trigger the reading of the two inputs: the total average and the eigenvolume of choice using two bypass elements. The eigenvolume is modified by multiplication with the current linearfactor and than added to the average image. After successful calculation the linearfactor is modified with a calculate element. ​   ​
 +
 +  cow.linearFactor=cow.linearFactor+cow.stepsize
 +
 +In the second loop we calculate append all intermediates on the average structure to convieniently visualize the movement in the 3D viewer. Using a script we add the current linear Factor in the header of the calculated linear combination ​
 +
 +  temp = cow.io[0]
 +  temp["​linearFactor"​] = cow.linearFactor
 +  cow.io[0] = temp
 +         
 +and than simply loop over the append logic. ​
 +The resulting trajectory can be visualized in the 3D viewer. ​
 +
 +
 +
 +