Dear Support
 
Hello,
 
Congratulation to new version of DS!
 
But, this issue is related with DS 4.1 ^^;;
 
A customer send a sample files which he used for RMSD calculation.
 
I attached that file.
 
I checked the order of atoms. All order is same with each other.
But, you can find that we can’t calculate rmsd between 1^st molecule and 2^nd molecule.
 
Below is the error message. 
All Atom RMSD to model1_mini_model_1 1
 
Name                           Reference                      RMSD (A) 
model1_mini_model_1 1          model1_mini_model_1 1            0.0000
The following molecule(s) failed due to connectivity
not matching the reference ligand.
 
2|BMS790052|compound1-out|sdf|1|dock3|1 1        
7|BMS790052|compound1-out|sdf|1|dock8|1 1        
1|BMS790052|compound1-out|sdf|1|dock2|1 1        
4|BMS790052|compound1-out|sdf|1|dock5|1 1        
BMS790052                      1        
BMS790052                      1        
BMS790052                      1        
 
Use the Hierarchy View, and turn on the bond display,
(right-click in the Hierarchy View and select Display Bonds)
Each bond must be listed in the same order, although the bond order
of the bond is not significant. 
But, all the bond orders have no problem (same).
 
I tested another small molecule I drawn, but it can be calculated.
 
I wonder that why we cannot calculate RMSD for only this molecule.
 
Please let me know
 
Regards
 
Siu