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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 as possible before going anisotropically.
You might also want to include more reflections - with "SHEL 10 0.1" you
leave out all data with d>10A which might be quite a few important
reflections.
It is difficult to go into more detail without knowing the exact content
of the output (lst-files), especially in the second case where the
listing file tells you that something is wrong with the 'ISOR'-command.
Regards,
Tim
On 03/19/12 17:00, 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
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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