[buster-discuss] Error for rms gradient in Buster or Gelly after sanity check

[Thomas Womack]

Dear buster users,

The message 

' *** ERROR rms gradient is NaN - not a number'

is almost always caused by having two atoms in exactly the same place, often by inserting a water into a peak in coot twice.

The next release will regard this as a sanity error, with message

        1 dist=   0.00 idealD=   2.74 sigma=   0.20 abs(Delta/sigma)=   13.70
          Between atoms A|121:O (WAT) A|150:O (WAT)
          distance is exactly zero. So atoms are exactly coincident.
          Advice: check this carefully

Probably the easiest way to figure out which atoms are on top of each other is to use the ccp4 remark-500 tool: run 'r500 HKLIN my.pdb', which will produce a file 'rem500' containing a message of the form

REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   O    HOH A   121  -  O    HOH A   150              0.00

Hope this helps,

Tom Womack (Global Phasing)