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 file
to 1.0 (meaning that they can be refined freely starting at 1.0) rather
than the usual 11.0 (which means that they should be fixed at 1.0; you
can add 10 to a parameter to fix it). Another possibility is that Coot
has not understood a 'free variable' that has been used for e.g.
occupancy refinement. The small molecule people use other graphical GUIs
for SHELXL (shelXle, WinGX, Olex2, System-S, XSEED, Oscail, XSHELL etc.)
that make far fewer mistakes. The .ins files written by Coot should
always be checked carefully and if necessary edited before running SHELXL.
Best wishes, George
On 03/19/2012 05:00 PM, Lu Yu wrote:
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 using coot to read in .fcf and .res file, and after model
building, coot can generate an .ins file. I was using this .ins file
and the original .hkl for the next round of SHELXL, except I added one
line "ANIS" in the .ins file:
"DEFS 0.02 0.1 0.01 0.04
CGLS 10 -1
SHEL 10 0.1
FMAP 2
PLAN 200 2.3
LIST 6
WPDB 2
*ANIS*"
I checked the working .ins and not-working (generated from coot) .ins
files,
1)*the working .ins* (generated from .res file at the very beginning)
has:
"WGHT 0.100000
SWAT 1.352762 2.1931
FVAR 2.6206 0.5 0.5 0.5 0.5"
2) *the not-workind(generated from coot) .ins* has:
"WGHT 0.1
FVAR 1.00000"
*The refinement is shown as follows:*
"Read instructions and data
** Warning: unusual EXTI or SWAT parameter **
** Warning: 8 bad CHIV instructions ignored **
Data: 6342 unique, 0 suppressed R(int) = 0.0000 R(sigma)
= 0.0615
Systematic absence violations: 0 Bad equivalents: 0
wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690
parameters
GooF = S = 4.279; Restrained GooF = 5.862 for 2243
restraints
Max. shift = 0.259 A for O_1131b Max. dU =-0.409 for O_1131b at
06:08:24
wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690
parameters
GooF = S = 12.229; Restrained GooF = 12.221 for 2243
restraints
Max. shift = 0.175 A for O_2131a Max. dU =-0.157 for O_5017 at
06:08:25
** REFINEMENT UNSTABLE **"
The other peptide dataset also has similar problem:
I was using coot-SHELXL, model building - refinement cycle
*successfully for the first 3 rounds*, but then, it gave me an error
message:
"Read instructions and data
** Warning: unusual EXTI or SWAT parameter **
** Warning: no match for 1 atoms in CONN **
** CANNOT RESOLVE ISOR .. O > LAST **"
I checked the working .ins and not-working .ins files (both generated
from coot this case),
1) the *working .ins*:
"WGHT 0.100000
SWAT 1.288932 3.0398
FVAR 2.6472 0.5 0.5"
2) the*not-working .ins*:
"WGHT 0.100000
SWAT 1.344708 3.0452
FVAR 2.731 0.54231 0.5409"
I was really confused, since I was using coot for model building for
other datasets, and the .ins file generated from coot is good for
SHELXL, but it didn't work all the time, eg. it work for the first few
rounds, then there is a problem.
Can you give me some suggestions about what I should do to get the
SHELXL running again?
Thanks,
Lu
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
