I had a similar problem with iMosflm, it ran nicely then crashed during
the integration stage. In the best possible traditions I then read the
instructions and added the following;
setenv MOSFLM_WISH /path/to/wish
setenv MOSFLM_EXEC /path/to/ipmosflm
setenv GFORTRAN_UNBUFFERED_ALL 1
The first two
Dear Afonine,
Thanks for your kind help.
Best wishes.
On Fri, Jul 31, 2009 at 10:38 AM, Pavel Afonine wrote:
> Hi,
>
>all the errors go into B and so you can get decent R with wrong
>> structure. Glycosylated proteins have a large component totally disordered -
>> do you see any sugars?
>>
Hi,
all the errors go into B and so you can get decent R with wrong
structure. Glycosylated proteins have a large component totally
disordered - do you see any sugars?
with B~133 you uj is 3.7A which means that atom is all over the
place and meaningless
As a reviewer I wo
Is it the gui or mosflm itself that crashes? The new gui is dependent
upon a number of external dependencies, so you are at the mercy of the
stability of those. The old gui still works fine, at least last time I
checked.
On Thu, July 30, 2009 4:40 pm, Marius Schmidt wrote:
> We have a little
Dear Marius,
'crash' is a very general term. Maybe you could describe at what stage
imosflm crashes? Is it reproducible or does it crash at random stages?
When you start imosflm from a terminal, what are the last words printed to
the terminal? Are there any log-files that might give a hint as t
Dear Vonrhein,
On Fri, Jul 31, 2009 at 12:47 AM, Clemens Vonrhein <
vonrh...@globalphasing.com> wrote:
> Dear Jiamu,
>
> On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote:
> > I am refining a structure of a complex between of 50kD protein and a 20kD
> > glycosylated protien. The data is of
Dear Ewa,
I can model a 3 residues sugar chain in the glycosylated protein. The
structure was build with an identical 2.3 A resolution structure as model.
The final structure is nearly identical with its model. So I think the model
is not wrong. The data was collected at 100K. During the refinement
We have a little internal project
where we want to compare the quality of
data reduced with HKL2000 and
IMOSFLM (mosflm) to 1.3 A. Unfortunately, imosflm
with its standard settings crashes always
even at lower resolution whereas HKL2000
is rock stable.
Why is that so? Any experience with that?
At ALS, we have a box of foils from EXAFS Materials that seems to get
passed around from beamline to beamline. I ran absorption scans on 17
edges from the metals in the box one day, and found that there was
considerable scatter in the expected vs observed edge positions:
http://bl831.als.lbl.g
Just got this working on a machine with a Quadro FX 3800. Stereo looks
great on both Pymol (v1.1) and the latest build of WinCoot (v0.6 build
2172).
On Fri, Jul 17, 2009 at 1:20 AM, Warren DeLano wrote:
> FYI, for folks not subscribed to pymol-users:
>
>
>
> nVidia today released beta drivers
On 00:00 Fri 31 Jul , Jiamu Du wrote:
> Dear All,
> I am refining a structure of a complex between of 50kD protein and a 20kD
> glycosylated protien. The data is of 2.9 A resolution. The wilson B factor
> is as high as 86.3 A^2.
> The refinement seems well with R/Rf of 0.21/0.25. But the B-fact
POSTDOCTORAL FELLOWSHIP IN PROTEIN CRYSTALLOGRAPHY AT KAROLINSKA INSTITUTET
As part of a collaboration between the laboratories of Rune Toftgård and Luca
Jovine at the
KI Department of Biosciences and Nutrition and the Center for Biosciences, a
postdoctoral
position is immediately available on
Jiamu Du schrieb:
Dear All,
I am refining a structure of a complex between of 50kD protein and a
20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B
factor is as high as 86.3 A^2.
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is
extra high. For the 50k
Huiying Li wrote:
I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters
to the refined structure. Often for the well ordered water sites the
routine added two water molecules in single water site, with their
distance (~1 Angs) way shorter than allowed hydrogen bonding distance.
I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters to
the refined structure. Often for the well ordered water sites the
routine added two water molecules in single water site, with their
distance (~1 Angs) way shorter than allowed hydrogen bonding distance. I
have to remove th
I am using TLS refinement with Phenix for the structure refinement.
On Fri, Jul 31, 2009 at 12:00 AM, Jiamu Du wrote:
> Dear All,
> I am refining a structure of a complex between of 50kD protein and a 20kD
> glycosylated protien. The data is of 2.9 A resolution. The wilson B factor
> is as high
Dear Jiamu,
On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote:
> I am refining a structure of a complex between of 50kD protein and a 20kD
> glycosylated protien. The data is of 2.9 A resolution. The wilson B factor
> is as high as 86.3 A^2.
> The refinement seems well with R/Rf of 0.21/0.2
Hi Jiamu,
My question is:
1. How to reduce the B factor to a reasonable level?
3. In the same of similar resolutionIs, is there some other structures
like this situation?
POLYGON tool is (one of) your friend(s) to answer this question (apart
from debatable one about "a reasonable level"):
Dear All,
I am refining a structure of a complex between of 50kD protein and a 20kD
glycosylated protien. The data is of 2.9 A resolution. The wilson B factor
is as high as 86.3 A^2.
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra
high. For the 50kD part, the average B f
Hi Elad
You don't say which version of Refmac you are using but I think the first thing
to do would be to try the latest version (5.5.0102). You can pick this up from
ftp://ftp.ccp4.ac.uk/nds/windows/refmac_5.5.0102/refmac5.exe
Copy this exe file to the bin subdirectory of your CCP4 installa
Dear all,
I am refining a structure in Refmac at 2.2 A in win OS. However,
Refmac failed and send this message: forrtl: error (72): floating
overflow
Thank you in advance for your any helpful suggestions.
Best,
Elad
Elad Binshtein
Ph.D student
Department of Life Science
Ben G
21 matches
Mail list logo
