Rather hard to advise!
Options are:
a) The helical domain is wrongly positioned!
b) There are scaling problems or swathes of missing data which can
depress some parts of the electron density. If you use coot and reduce the
contour level in this region, is anything sensible visible?
A useful
Hello All,
I am new to low resolution refinement parametrization and regularization.
Crystal diffracted with high anisotropy reaching to 3.5A in one direction
and 4.5A other direction. I am refining a structure at 3.9A resolution.
Protein has two domain connected trhough a linker and is packed as
At this resolution it is very much possible to choose a wrong space
group. So try lower symmetry first and see if it helps. Check for
twinning too.
On Sat, 2011-01-08 at 19:08 +, Dimitris Ladakis wrote:
Dear all
I've got a 3A dataset processed with mosflm and scaled. I've
runned MOLREP
Dear all
I've got a 3A dataset processed with mosflm and scaled. I've runned MOLREP that
gave a solution with a score of 0.52. At this stage the Rfactor was 44%.
After my first round of refinement with REFMAC i've got both Rfactor and an
Rfree at about 43%. After model building and several
Dear D.L.,
I suspect the issue is in determining the correct space group. Sharing the
Rmerge and current space group would be useful.
Take Care,
Sean
http://store.p212121.com/
Dear CCP4ers,
I refined a 3.4 A SAD data in refmac ( using the 'SAD data directly' option
) and reached a plateau with an Rfree of 36%. Then I tried to extend phases
with the 2.95 A dataset which has no anomalous data (I maintain the same
Rfree flag). The maps look like a moderately good fit, but
Hi Sampath,
On Sat, Jul 26, 2008 at 02:05:17AM +0900, Sampath Natarajan wrote:
Also I could find many cuts in the density.
This looks to me like a problem with your low-resolution data? Since
you collected 1.6A data my guess is that you probably had a fair
amount of overloads. Did you do a
Dear all,
Now I'm solving a structure with 1.6A resolution. The data seems good with
R-sym (12.4) and all other parameters. Actually the data was collected with
SAD phasing. When we checked the data we couldn't find the Se atom in the
structure. Since the data resolution is good, we tried to do
that w
ell, my maps are 5A resolution, so I don't worry about that option.
Mark
-Original Message-
From: Sampath Natarajan [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 25 Jul 2008 11:05 am
Subject: [ccp4bb] Refinement problem
Dear all,
Now I'm solving
From: Ta Hai
Sent: Sat 7/26/2008 3:00 AM
To: Sampath Natarajan
Subject: RE: [ccp4bb] Refinement problem
With the R and freeR factor 45.3% and 51.4%, I'm quite sure that your MR
solution is not correct. Although your current model seems fitting with the
map, but it's just the biased map after
Hi,
I have one structural refinement problem.
I am working on a protein crystals which diffracted to 2.8 Å. But when I
refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get high
B-factors around 70. But if I do TLS refinement, the R-factors lower
down and B-factors come down
parkash wrote:
Hi,
I have one structural refinement problem.
I am working on a protein crystals which diffracted to 2.8 Å. But when
I refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get
high B-factors around 70. But if I do TLS refinement, the R-factors
lower down and
Hi,
It would be nice if you mention more clearly how you have done
TLS..i.e.,domains or individual residues or molecules !! You should keep in
mind that you have 2.8A data. I would do TLSANL with domains or molecules.
Best regards,
Krishna Ch
PhD Student
Hannover Medical school
Germany
On
Hi,
It's much easier to begin with the cif file created by Refmac5
itself, but this cif file needs to be checked and corrected
manually for the restrains. Certainly, Iodine is not happy
with the current restrains.
Most of the time, i have found problems beginning with the
protonation and
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