Dear Wenhe,

No 3D superpose tool will always align/map all Calphas. If in the one protein the loop turns left, and in the other it turns right, then mapping those loops is meaningless and thus not done by good software. The other problem is that often two proteins that get compared do not even have equally many residues so that there will always be some unaligned/unmapped Calphas left at the end. Look for some articles by Arthur M Lesk on this topic, he has explained protein superposition (problems) very clearly.

Gert

Ps, if you want proteins superposed and get different output from what the standard software gives you, just mail me those PDB files and I can see what I can do.


On 29-10-2016 17:47, WENHE ZHONG wrote:
Dear all,

I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I 
want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph 
(instead of using the graph automatically made by the program). However, there 
are many atoms missing in the RMSD list.

In the settings I chose “Superpose specific atoms/residues”, checked “Output 
all distances to a file”, fit “C-alpha atoms”. The superposed structures have 
exactly the same sequence.

My question is: is there any way to get the completed list of RMSD value for 
each C-alpha atom? Or is there any other program for this purpose?

Thank you!

Kind regards,
Wenhe

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