Dear All:
I try to run xds in linux, but have some problems.
With xdsconv, it complains:
f2mtz: error while loading shared libraries: libccp4f.so.0: cannot open
shared object file: No such file or directory
cad: error while loading shared libraries: libccp4f.so.0: cannot open
shared object file:
Shape of the diffraction spots changes in the statistical disorder <-->
> twinning continuum. At both ends spots shape is like in diffraction from
crystals without such disorder. However, in the intermediate case,
electron density autocorrelation function has additional component to
one resulting f
UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF)
RESEARCH SPECIALIST, JURA LAB
A research specialist position in Receptor Tyrosine Kinase Structural Biology
is available immediately in the lab of Prof. Natalia Jura at the University of
California, San Francisco (UCSF). The Jura Lab merges structural
Hi Nic,
There is no reason that you have to use the Unity desktop at all. I prefer
using the XFCE4 desktop myself. It is easily installable from the Ubuntu
repositories and then you just have to select it at login. In one of the
xfce4 settings options ("Window Manager Tweaks") you can disable d
Hi Nic,
There is no reason that you have to use the Unity desktop at all. I prefer
using the XFCE4 desktop myself. It is easily installable from the Ubuntu
repositories and then you just have to select it at login.
Cheers,
Rob
On Tue, 2014-03-11 14:44 EDT, Nic Steussy wrote:
> Matic,
>
> I
Matic,
I am struggling with Ubuntu on this issue.
The Nvidia driver needs the 'Composite' function disabled in order
to function in 3D. This required the use of the Unity-2D package
to disable the 3D used in the Ubuntu desktop effects. This worked
Hi, all,
I would like to get an idea on which software packages can be used for
predicting the structures of membrane proteins? What about single-pass?
Many thanks for your input,
Jiang
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If you refined with REFMAC - I look at the log graph under R factor v
resolution.
The second plot isd v - obviously they should overlap but
sometimes they dont, indicating scaling problems!
What is yours like?
On 11 March 2014 14:16, Amlan Roychowdhury wrote:
> Hello Eleanor,
>
> The resolut
Hi,
If there's an NCS translation, recent versions of Phaser can account for it and
give moment tests that can detect twinning even in the presence of tNCS. But I
agree with Eleanor that the L test is generally a good choice in these cases.
However, the fact that you see density suggests that
Hello Eleanor,
The resolution was 2.7 A and final R/Rfree = 19/23
The model was complete. water molecules were added.
The green elongated density was present at the periphery of the protein.
Regards
Amlan
On Tue, Mar 11, 2014 at 6:53 PM, Eleanor Dodson
wrote:
> You dont say what resolution you
Sorry - hadnt finished..
The twinning tests are distorted by NC translation - usually the L test is
safe, but the others are all suspect..
On 11 March 2014 14:09, Eleanor Dodson wrote:
> What is the NC translation? If there is a factor of 0.5 that makes SG
> determination complicated..
> Elean
What is the NC translation? If there is a factor of 0.5 that makes SG
determination complicated..
Eleanor
On 11 March 2014 14:04, Stephen Cusack wrote:
> Dear All,
> I have 2.6 A data and unambiguous molecular replacement solution for
> two copies/asymmetric unit of a 80 K protein for a cry
Dear All,
I have 2.6 A data and unambiguous molecular replacement solution
for two copies/asymmetric unit of a 80 K protein for a crystal integrated
in P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9.
Refinement allowed rebuilding/completion of the model in the noraml way
but the
Dear Monica,
for refmac5 this is nicely explained at
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Occupancy
Best,
Tim
On 03/11/2014 12:14 PM, Monica Mittal wrote:
> Dear Sir
> May i know how to refine the group occupancy for a ligand???
>
> Thanx in advanc
Dear Sir
May i know how to refine the group occupancy for a ligand???
Thanx in advance
On Mon, Mar 10, 2014 at 2:11 PM, wrote:
> Dear Amlan,
>
>
>
> The sigma of an Fo-Fc map map depends on the residual noise in your map. In
> a well-refined structure, the sigma will be low, so at 3 sigma it wi
You dont say what resolution you are working at, or what the current R
factor is. or how complete the model is.
There are assumptions made in the refinement scaling algorithms and in
their treatment of supposedly poorly ordered solvent which can generate
false density (both positive and negative)
Dear all:
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Dear All,
Thank you very much for your reply.
I have an another doubt and I want to discuss with you.
Sometimes for some structure during refinement and model building we have
found a green blob (Fo-Fc and >5 sigma).
If I scroll down the blue 2Fo-Fc map to a very low sigma level nearly at
0.5 a r
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