Hi Pankaj,
if you are refining in phenix.refine:
- is automatic ordered solvent (water) update is turned on;
- you can try weight optimization: "optimize_wxc=true optimize_wxu=true";
- is NCS available. Use it if so.
In fact, the Rworks seems fine, but the gap Rfree-Rwork seems large.
Insignif
Hi all,
In one of my 2.52 A structure, which is dimeric, the R-factor is 21.4 and
free-R is 29.3. I have tried all ways to reduce the free-R including TLS
(even by defining the number of TLS group per chain), but still factors are
not getting reduced. Even i have tried some other space group, but
Frederic VELLIEUX wrote:
Hi Rui,
Use the control key (pressed down) to translate the map and get the center
point on top of your positive density (using the mouse at the same time, left
button I think). Do not hold cntrl any more to rotate the map by 90 degrees.
Cntrl again to move the map e
Thank you all for the quick reply. Kim and Ingrid both pointed me to the
same direction!! Thanks a bunch :-)
On Thu, Dec 3, 2009 at 2:37 PM, Frederic VELLIEUX <
frederic.velli...@orange.fr> wrote:
> Hi Rui,
>
> I am at home so this is all from memory. In coot.
>
> Use the control key (pressed dow
Hi Rui,
I am at home so this is all from memory. In coot.
Use the control key (pressed down) to translate the map and get the center
point on top of your positive density (using the mouse at the same time, left
button I think). Do not hold cntrl any more to rotate the map by 90 degrees.
Cntrl
Hi, All,
I tried to use phenix to add water molecules, and when I check those waters
in coot, I can easily delete them if they are not in right spot. However, if
I see some clear positive maps that seems like water, can I add manually at
that position? How to do this in coot?Or any other way?
Rwork = 0.26 and Rfree = 0.32 are not necessarily unacceptably high
for a 2.3 A dataset in my opinion.
Not all crystals are the same, some just have more disorder than
others and not all of this disorder is modelable (if that is a word).
Having said that:
- is the 2.3A data cutoff perhaps a ta
Hello-
I am working up a data that is giving me unacceptable high R factors.
I am solving a data set that is good to ~ 2.3 Å using molecular
replacement based on a previously crystalized variant. The maps look
good with all the density fitting well to my model. I originally
worked up the
Before you all go away and install the latest Intel compilers to fix
this bug - don't bother! We just installed the latest version (ifort
11.3) and it has the same bug! We plan to file a bug report with Intel.
In case anyone is interested, this is the code snippet which exhibits
the buggy behavi
Discussing with Fred Vellieux offlist I suggested the following: would it be
useful to have a sort of 'simulated annealing' of the B-factor values? - in
refinement I often try resetting them to higher values (Moleman has a function
for this I think) and then see which ones refine back down nicel
Hi Megha,
You could make your buffer solutions at room temperature, so
that the 8M urea dissolves completely. During solubilization of the
protein, keep the tube on a shaker or agitate the solution using a magnetic
strirrer. This will prevent any crystallization of the urea. In any case,
urea c
Hi Meg
I would highly recommend giving 6M guanidinium chloride a go in parallel, to
compare the solubilization efficiency of the two approaches. We have had a
couple of cases in the lab where homologous proteins showed strong
preference either to urea OR guanidinium chloride when it came to
solubil
Hello,
I would be interested in people experiences and opinions about what
types of fluorescence microscope setups have worked
adequately to distinguish small protein crystals from background/
autofluorescence etc. ...general comments?
(regular dichroic mirros etc dont allow Trp peak to pass t
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