Hi all,
I was using SHELXL for the refinement of a small peptide molecule (6-7
residues), and it was working for the first round. But then it gave me an
error message. I don't know what's going on and have you had the same
problems? Can you give me some suggestions?
*For more information*:
I was
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Dear Lu Yu,
your wR2 in the first log-extract seems very high (43%) - it might
simply be that you model is still not good enough to refine the data
anisotropically.
Does it work if you refine the model isotropically? If so, improve the
model as much
Dear Lu Yu,
SHELXL is usually very stable so there must be an error in your .ins
file, but it is difficult fo us to guess what it is without seeing the
full file. A common error that can cause such instability is caused by a
long-standing bug in Coot, which sets some occupancies in the .ins
You dont say at which point in the refinement cycle you are..
The refinement algorithms are meant to reduce these parameters, and if
they diverge wildly there is probably something seriously wrong either
with the software or the model..
eg - different cell dimensions or space group for the
...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Clemens Vonrhein
Sent: 13 February 2009 17:15
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unstable refinement
* you don't mention if the R and Rfree move up identically - or if you
have a faster increase in R than in Rfree
Rfree-R), or a combination of
factors.
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Clemens Vonrhein
Sent: 13 February 2009 17:15
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unstable refinement
), making your model overfitted
after the fact!
Cheers
-- Ian
-Original Message-
From: George M. Sheldrick [mailto:gshe...@shelx.uni-ac.gwdg.de]
Sent: 16 February 2009 11:24
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unstable refinement
Dear Ian
!
Cheers
-- Ian
-Original Message-
From: George M. Sheldrick [mailto:gshe...@shelx.uni-ac.gwdg.de]
Sent: 16 February 2009 11:24
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unstable refinement
Dear Ian,
That was in fact one of my reasons for only calculating the free R
Hi,
I would like to survey the group for causes and potential solutions to
unstable refinement (the steady and upward drift of R and Rfree in each
cycle of refinement). I am currently aware of the following potential
causes: twinning (meohedral, pseduomerohedral, or epitaxial), anisotropy,
John,
I would argue with the statement that a steadily increasing Rfree
denotes an unstable refinement. This could be due to the fact that your
initial model is biased by information not in your data. This would
include previous refinement against the TEST set, use of a high
resolution MR model
Hi John,
Just to play devils advocate (is that the right terminology?), a
random list of potential issues that could cause that .. seen that,
been there, suffered ...
* Rfactor tells you something about your X-ray term, so if you have
the weight on the X-ray term too low (or the weight on
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