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J. Dunbar jlh at BOGOSITY.CHEM.PSU.EDU
Thu Oct 10 16:53:38 EST 1996


Hello, X-PLOR Users.

I have a quick question regarding the dependence of B-factor on XPLOR 
version.  I have been using X-PLOR 3.1 for my refinement up until this week.
I have a protein structure which is basically finished.  I had to make a
minor change in the position of two added glucoses so I ran a final round of
refinement with X-PLOR 3.843.  I did not make any alterations in the protein
structure between the last round of refinement and this.  The Rfree and
Rcryst both dropped by about 1%, but the average B-factors for the protein
increased by about 6 A**2.  I now have some main-chain atoms with the
maximum (grouped) B-factor of 100.  The B-factors for the glucoses increased
by a similar amount, but the water B-factors increased very little.

Is there some difference between the versions which is introducing artifacts
into my B-factors?  When I tried to run bgroup with my old input file it
abandoned the line search after 6 cycles (nstep=15) without having R factors
converge or calculating new B factors.  I used the new bgroup.inp script
and it worked fine, but gave me these higher B-factors.  Any suggestions
as to the potential problem or even if I should be concerned would be 
appreciated.  I was previously running XPLOR on a remote system and would
really like to be able to use version 3.843 on our new computer.

Thanks in advance for your help.

Jennifer Dunbar


***********************************************************************
  Jennifer Dunbar                  e-mail: jlh at bogosity.chem.psu.edu
  Dept of Biochemistry             Phone:  (814) 865 8383
  Althouse Laboratory              Fax:    (814) 863 7024
  Pennsylvania State University
  University Park, PA 16802
  USA
***********************************************************************





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