No comments on much of your message but I cannot believe you can get better
results by cutting anisotropic 2.1A data to 3.3A!!
You MUST be throwing away valuable experimental information,, remember
crystallography is not about getting low R factors but about getting a
model consistent with you
Not an answer, but if you look at the Wilson plot after scala or truncate,
you can see how good the estimate is - at 3A those can be pretty awful
Eleanot
On Mar 5 2012, anna anna wrote:
Dear all, I hope you can help me!
I solved a structure at 3.0 A res and everything is quite satisfactory, m
Dear Tim,
good catch, thanks; I could craft that phrase more carefully! Although
often it may not be quite fair to take phrases out of context: this
newsletter article was written in the context of macromolecular refinement.
And yes, "recently" may be a broad term -:)
All the best,
Pavel
On Mon,
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Dear Pavel,
you may want to add to the structures mentioned in [1] one or two
organic structures present in the Cambridge Database.
"Until recently it was customary to ignore hydrogen atoms throughout the
process of crystallographic X-‐ray structure
Hi,
On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin wrote:
> Adding the riding hydrogens generally gives you some improvement in R
> factors even with a good quality (i.e. stereochemically correct) model.
>
and here are the results of more or less systematic test that prove this:
see "On cont
On the interface under Refinement Parameters there are three options
1) Use if present
2) Do not use
3) Generate all
if you are using script then default is generate all (add them riding
positions). You can switch to other options:
make hydr all# generate all - default option
make hydr yes #
Hi Paul -
Refmac does indeed add riding hydrogens by default; see here:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/restraints.html#makecif
The REMARK 3 is referring to what you think it is: riding hydrogens have
been added. (They are not, however, written to the output file unless
you
Hello CCP4 community,
I'm posting at large regarding a previously raised issue for REFMAC for which I
cannot find the conclusion in the old threads.
Specifically, does REFMAC add riding hydrogens during default refinement?
Though I've not requested that any hydrogens be added, only used if in t
Dear All,
Thanks for all the suggestion. Data is anisotropic. Since anisotropic
correction with the UCLA server didnt give any good Molprobity scores and
didnt reduce the R/Rfree at 2.1A, I am using ~3.3A data for further refinement.
Using Tom's suggestion of target restrains reduced the gap b
Dear all, thanks for help!
I'm using Refmac without TLS.
Tim's explanation is pretty convincing to me. My data have no ice rings
compromising the extimation of I, but the map, is more defined then I
expect at 3 A resolution, so a "low" average B seems consistent. Which can
be other causes for lim
Hi,
Please see a similar thread at ccp4bb earlier at the following link
http://www.proteincrystallography.org/ccp4bb/message16011.html
Padayatti
2012/3/5 anna anna :
> Dear all, I hope you can help me!
> I solved a structure at 3.0 A res and everything is quite satisfactory, my
> only concern is
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Dear ,
the Wilson plot is only meaningful with data better than 4A. Since your
data extends to only 3A (and according to your I/sig(I) stats you pushed
that limit a little...), you may have too little data for a good fit.
That's only one possibil
Dear all, I hope you can help me!
I solved a structure at 3.0 A res and everything is quite satisfactory, my
only concern is the discrepancy between
the B factor from Wilson plot (58.8 A^2) and the average B (36.9). It seems
strange, usually the opposite occurs...
What does it mean? Which may be th
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