Hi again,
Thanks for your insight into refinement tools for twinned data. I have a
couple of twinned data sets that are nearly perfectly pseudomerohedrally
twinned. I've begun to refine my data in Refmac5 (using the automated twin
refinement), CNS (using the twin inputs) and Shelxl; I'm testing
Dear Tim Fenn,
That's better : )
On Mon, 16 Mar 2009 11:01:34 +0800
Sheng Li biol...@gmail.com wrote:
Please read the coordinate file with alwyn's O, and then save it to
another file. The ANISOU lines will be removed.
only if you use s_a_i - pdb_read will preserve ANISOU.
It might be
Dear friends,
if the data is of high enough resolution, wouldn't be more reasonable to
attempt anisotropic refinement (constrained with TLS or refining
individual anisotropic ADP), or mixed one - some atoms are isotropic and
some anisotropic, rather than struggle with file conversions and
The deposition of images would be possible providing some consistent
imagecif format was agreed.
This would of course be of great use to developers for certain
pathological cases, but not I suspect much value to the user community -
I down load structure factors all the time for test purposes
I am not sure if there is any way of avoiding model bias if the
coordinates are included regardless of whether there is twinning or not
- my preferred method is to set the occupancies of suspect regions to
0.00 then do refinement of the better parts of the model and then check
maps again and
Hi
I'm afraid the adoption of imgCIF (or CBF, its useful binary
equivalent) doesn't help a lot - I know of three different
manufacturers of detectors who, between them, write out four different
image formats, all of which apparently conform to the agreed IUCr
imgCIF standard. Each
Hi Walter,
You should definitely detwin data for map calculation if you have a
significant twinning fraction (and only for maps; keep using the twinned
data set for refinement). We use the CCP4 program detwin. BUT if Shelxl
gives bad density, maybe that's simply what you have, a bad density map -
Hi -
I thought that both phenix and refmac output map coefficients
corresponding to de-twinned data - or do I get this wrong?
I am also wondering what is the context of poor and if it has to do
with twinning,
or simply if the starting model is not so good. In what was are these
poor maps
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**ESRF-EMBL, Grenoble, France, 15 - 19 June 2009
An EMBO / MAX INF2 2009 course on Structure Determination in
Macromolecular Structure will be hosted by the ESRF in Grenoble,
France from 15 to
Dear Colleagues,
The issue Harry is describing, of people writing multiple variations of
image formats even though all of them are imgCIF is not really a
problems with the images themselves. Rather it is a lack of agreement on
the metadata to go with the images. This is similar to the
But dont all twinned refinement programs output detwinned terms for a map?
Certainly REFMAC and SHELX do.
Eleanor
Clemens Steegborn wrote:
Hi Walter,
You should definitely detwin data for map calculation if you have a
significant twinning fraction (and only for maps; keep using the twinned
As far as I know map coeffiicient correspond to detwinned data. But
using detwinned data may not be a good idea.
It would be good to see what are R factor. Another thing to consider
is that different program may use different flags for free R and it
may cause some problem.
What are Rfactors,
Yes, Phenix default output (for twinned data) is detwinned, like the one
from Shelxl; didn't know for the new Refmac twin option - but I understand
from this posting and Garib's that it also detwins if the twin option is
used ...
So considering that the Shelxl-derived density looked bad, I
But wouldn't detwinning be problematic with nearly perfectly twinned
data? I'll post my own question about separately to not hijack the
thread...
On Mon, 2009-03-16 at 11:24 +0100, Clemens Steegborn wrote:
Hi Walter,
You should definitely detwin data for map calculation if you have a
Some time ago, I had a dataset which turned out to be P31 with a dimer
sitting on the three-fold axis. The only way I found to process it was
to run twinned refinement in CNS with (-h,-k,l) and twinning fraction of
0.5. R/Rfree are 20/24% at 2.4A resolution, so the model must be right
at least
Dear all,
I am trying to compare several related structures using LSQKAB. In
order to refine the superpositions, I'd like to use the option
radius, to see the relative postion of certain residues within a
given distance from a common point.
The programme reads the commands OK:
ALL
Hi everyone,
Recently, I obtained a soluble glyco-protein. Unfortunately, after I added
PNGase or Endo Hf to remove the glycans, the deglycosylated protein is
precipitated. Is there any method to avoid this kind of precipitation?
Thanks,
Simon
Hi Simon,
Although they are a source of heterogeneity for
crystallization, glycosylations usually stabilize proteins.
There are a couple of things that may be important to consider before you
deglycosylate your protein.
Do you know how many natural sequons/glycosylation sites your protein has?
My apologies Simon, I should have been more thorough answering your
question.
Yes the protein was shown to be quite homogenously glycosylated using
mass-spectrometry.
The ED maps showed the first two ordered fully occupied NAG units and
residual density for a third sugar unit although it is very
Dear Norman,
That did the trick! And was easy to do...
Thanks a lot,
Anita
Dear Anita
You could try adding the following additional line of input:
rotate matrix 1 0 0 0 1 0 0 0 1
This multiplies the data in XYZINM by the identity matrix (so that
the data should be unchanged) but has the
Dear Simon,
this may be an isolated case, but you might want to try to drastically
change the pH of the reaction conditions.
In our hands, a protein with 3 hyperglycosylated sites, expressed in Pichia
pastoris, could be deglycosylated readily with endoH. However, at the
recommended reaction pH
Hi all,
I am trying to fit a ligand into density using ARP/wARP 7.0.1 in CCP4 suite
6.0.2 on CCP4interface 1.4.4.2.
I get an error message telling me to look for the error in a
##_warp_ligand_details.log.
_
Running Refmac5 to refine
Dear All
I am refining proitein-DNA complex structure in
Refamac5. When I used coordinate file containing 2
bases less, then the refinement is running smoth and
perfect. But when I built 2 exta bases to the existing
DNA in the coot then refinement is failed with the
following error message.
Hi Rajkumar,
Few days back similar problem was happening to me also.
I just changed the version of Coot and it worked.
In my case only Coot (ver. 4.1) was doing the job correct.
Please try Coot (version 4.1) in case you are using any of other versions.
HTH,
Y
On Mon, Mar 16, 2009 at 11:43
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