clean vrs. clean:full

 

Hi,

We compare standardizer "clean" to "clean:full" .. we prefer "clean" because it retains the original molecule orientation, but notice that "clean:full" does better cleaning.

After cleaning, we run OverlappingAtomsChecker, OverlappingBondsChecker, BondAngleChecker(2.5), and BondLengthChecker.

For 1735 structures, after "clean":

 163 Structure problems:  Bad bond lengths found

   2 Structure problems:  Overlapping atoms found

   6 Structure problems:  Overlapping atoms found; Overlapping bonds found

  76 Structure problems:  Overlapping atoms found; Overlapping bonds found; Bad bond lengths found

  72 Structure problems:  Overlapping bonds found

   2 Structure problems:  Overlapping bonds found; Bad bond angles found

  78 Structure problems:  Overlapping bonds found; Bad bond lengths found

(total = 399)

 

For same structures, after "clean:full":

 160 Structure problems:  Overlapping atoms found; Overlapping bonds found

   2 Structure problems:  Overlapping atoms found; Overlapping bonds found; Bad bond lengths found

  82 Structure problems:  Overlapping bonds found

(total = 244)

 

Is there a way to get better cleaning of "clean:full", while still retaining orientation of structure?

Thanks.

Andrew

 

Hello,

Sorry for the late answer, we are investigating the issuee. We need some more time to find the cause.

Regards,

Erika

Hello,

Could you send us the structure please?

 

Regards,

Erika

I will try to collect some examples .. thanks

Hi,

Actually "clean:full" takes the whole molecule and generates new coordinates for the atoms, while "clean" fixes the coordinates of the atoms which are not modified during the standardizer transformation and tries to partially clean the modified atoms.

It is not possible to use "clean:full" in the partial clean sense, but we can look into the problems you faced with the "clean" and try to fix them.

Thanks .. I've collected some examples for our meeting.

 

Best,

 

Andrew