Hi Jiamu,
OASIS may help solving your problem. We have example on solving an
originally unknown protein (1086 residue in the AU) at 3.3A resolution with
Se-SAD data (redundancy=3.3). The process involved SAD-iteration and
MR-iteration with OASIS. If you need help, we can discuss off list.
Cheers
You can use Refmac to take your SAD information (F+ and F-), heavy atom
and MR model directly and refine both your Se sites and your MR model
simultaneously. This function in Refmac has been around for 'more years'
and is what has been re-implemented in a mathematically equivalent form in
Phas
Hi Jiamu,
to complete the Juergen answer, that's true that the MR-SAD approach is very
powerful and can definitely help in your case. You can use Sharp and add the
information from your partial molecular replacement solution encoded as HL
coefficients and do a MR-SAD phasing.
Here is the procedu
Hi Jiamu,
this program can do it:
http://www.phenix-online.org/documentation/reciprocal_space_arrays.htm
Let me know if you have questions and we can discuss it (off-list).
Pavel.
On Tue, Jul 12, 2011 at 6:08 PM, Jiamu Du wrote:
> Dear All,
> I am now working on a low resolution phase determ
http://www.globalphasing.com/sharp/
or you could extend your phases using DM if you have more than one molecule in
the asu.
I'm sure there is also a way to convince solve/resolve to do what you want.
If you see enough in your map, just build a backbone model and use that to
generate a crude mask
On Tue, Jul 12, 2011 at 6:08 PM, Jiamu Du wrote:
> I am now working on a low resolution phase determination (around 3.3 A with
> Se anomalous signal around 3.8 A).
> I can find the Se site and get the phase, but the density map is not so
> good.
> Some part of the protein (about 1/3) has a homolo
Dear All,
I am now working on a low resolution phase determination (around 3.3 A with
Se anomalous signal around 3.8 A).
I can find the Se site and get the phase, but the density map is not so
good.
Some part of the protein (about 1/3) has a homologue model which is also can
be found using Phaser.
A couple of people asked why the GST/His steps. The only way I can expressed
this protein is by co-expression. Co-protein is GST tagged and my protein of
interest is N-term His and C-term StrepTag. Even with the coexpression, there
is a major degradation product, the reason why for the strep tag
Ha. That is obviously it. I failed to account for Brownian motion in the pdb
file itself. Properly modeling this is really going to mess with my data to
parameter ratio.
Katherine
On Tue, Jul 12, 2011 at 12:54 AM, James Stroud wrote:
> On Jul 8, 2011, at 11:13 AM, Katherine Sippel wrote:
>
> >
Dear All,
An updated ccp4i interface to Refmac 5.6 is available at:
http://www.ccp4.ac.uk/prerelease/refmac5_task_for_ccp4_6.2.tar.gz
You can do "System Administration -> Install/uninstall Tasks" from the
GUI, or just copy the individual files from the tarball to the
$CCP4/ccp4i area.
This int
I have attempted to use the RosettaDock webserver for protein-protein docking.
If I recall correctly, the webserver is only capable of doing fixed backbone
docking simulations. If you are docking a small peptide with a protein I
suspect you want the peptide to be somewhat flexible. Although my r
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