Re: [ccp4bb] lsqkab problem to be reported to developer

[Eleanor Dodson]

Can you send more details? the log file? the pdb


On 30 May 2014 22:54, Carter, Charlie car...@med.unc.edu wrote:

 This is a bizarre problem. I'm trying to superimpose multiple
 conformations of the same protein using segments I expect not to change.
 LSQKAB bails with this error each time:

  *** RWBROOK error: point code unitfunction
  ***1 -1022MMDB_F_Atom
  *** file   : 4ARC_rot.pdb
  *** reason : internal error #2 -- report to developer
  *** Execution stopped.

 It also appears very likely that the superposition is wrong. I expect an
 RMSD for the superimposed atoms (main chain only) of less than 2 Å, yet the
 program reports that the RMSD is 7 Å.

 Thanks to anyone for a diagnosis and prescription.

 Charlie

Re: [ccp4bb] lsqkab problem to be reported to developer

[Eugene Krissinel]

Charlie,

Most probably this indicates a problem with your PDB file, either a format or 
things like misplaced or absent residue name etc. If you can send me your files 
and exact command that you run, I can have a look into this.

In future, if you see a message like report to developer please send it to 
CCP4 group rather than BB, this will help to deal with it faster.

Many thanks,

Eugene


On 30 May 2014, at 22:54, Carter, Charlie wrote:

 This is a bizarre problem. I'm trying to superimpose multiple conformations 
 of the same protein using segments I expect not to change. LSQKAB bails with 
 this error each time:
 
 *** RWBROOK error: point code unitfunction
 ***1 -1022MMDB_F_Atom
 *** file   : 4ARC_rot.pdb
 *** reason : internal error #2 -- report to developer
 *** Execution stopped.
 
 It also appears very likely that the superposition is wrong. I expect an RMSD 
 for the superimposed atoms (main chain only) of less than 2 Å, yet the 
 program reports that the RMSD is 7 Å.
 
 Thanks to anyone for a diagnosis and prescription.
 
 Charlie


-- 
Scanned by iCritical.

[ccp4bb] lsqkab problem to be reported to developer

[Carter, Charlie]

This is a bizarre problem. I'm trying to superimpose multiple conformations of 
the same protein using segments I expect not to change. LSQKAB bails with this 
error each time:

 *** RWBROOK error: point code unitfunction
 ***1 -1022MMDB_F_Atom
 *** file   : 4ARC_rot.pdb
 *** reason : internal error #2 -- report to developer
 *** Execution stopped.

It also appears very likely that the superposition is wrong. I expect an RMSD 
for the superimposed atoms (main chain only) of less than 2 Å, yet the program 
reports that the RMSD is 7 Å.

Thanks to anyone for a diagnosis and prescription.

Charlie