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
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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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