[buster-discuss] Error for rms gradient in Buster or Gelly after sanity check
twomack at globalphasing.com
Wed Mar 3 16:55:52 CET 2010
Dear buster users,
' *** 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 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)
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