Dear Weifei,
You might want to use SUPCOMB from the ATSAS suite.
http://www.embl-hamburg.de/biosaxs/supcomb.html
Cheers,
Deborah.
SITUS is another good option.
R
From my iPhone
On 26 Jun 2015, at 08:20, Deborah Harrus har...@free.fr wrote:
Dear Weifei,
You might want to use SUPCOMB from the ATSAS suite.
http://www.embl-hamburg.de/biosaxs/supcomb.html
Cheers,
Deborah.
Dear Weifei,
in my experience you can try a couple of things:
* Use SUPCOMB which is a part of the ATSAS package
* Use SITUS to fit your structure into the envelope (SITUS can be downloaded
here: http://situs.biomachina.org and also contains a tutorial specifically for
this type of
Hi
Thanks all, I appreciate all the valuable inputs..
Piush..
I ll be trying Benzonase up next.. but since the DNA appears so secluded
for DNAses, it makes me little skeptical as mg and DNAse already been there
for ON dialysis.
Tim
if the DNA binds to the protein, wouldn't this
At low resolution, without interpretable anomalous signal, neither SAXS
nor molecular replacement with SAXS model, can distinguish correct from
inverted solution. So inverted model will fit crystal data equally well.
Only phase extension to much higher resolution (e.g. 5A) can help.
Yes,
That an entire 500bp would be protected from DNase seems very very strange -
but very interesting if true!
Could that band on the agarose gel be something else? Protein will stain a bit
with ethidium as well as with coomassie. Did you add SDS before running the
agarose gel or is it native
Dear Almudena,
I have some questions to help you, how many molecules are presents in the ASU ?
If more than one, maybe you can try to find NCS in the substructure. To perform
that it could be necessary to increase (more than 20) the radius of NCS
research parameters.
You can try to find NCS
Dear Weifei,
You'd better ask this question on phenixbb as here is ccp4bb.
But the environment variable file (.bashrc or .bash_profileis) in your home
folder(specific user) or in /etc/profile (all user). Source Phenix in this
file. Next time you run the terminal, the file will be
I'm trying to generate an oligomer using pdbset with the script attached below.
The rotated molecules appear to be oriented properly, but they cannot be viewed
correctly in PYMOL because the cartoon option fails to connect many of the
residues. What am I doing wrong?
Thanks,
Charlie
pdbset
That's interesting. Enantiomer differences can be detected at worse than
20Angstrom resolution in EM reconstructions. What do you think is the reason
for this?
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 12318
New York,
Hi Charlie -
I'm not able to reproduce your issue. I tried this with a random PDB and,
although the symmetry operation wasn't appropriate for that particular
structure, I got normal-looking cartoon representations.
One thing to consider might be that, if there are abnormalities in the
Do you need to rename the symmetry shifted chsain?
Eleanor
On 26 June 2015 at 16:33, Carter, Charlie car...@med.unc.edu wrote:
I'm trying to generate an oligomer using pdbset with the script attached
below. The rotated molecules appear to be oriented properly, but they
cannot be viewed
THESEUS can do it, and it comes bundled with ccp4 so definitely on-topic.
If you want RMSD of “equivalent” amino acids, you must tell THESEUS which
residues are equivalent with a sequence alignment. Then use the -I option to
get the RMSD (and other stats) of the pdb files in their current
Shouldn't the ability to distinguish enantiomers also depend upon the
degree of asymmetry of the particle itself? (or pseudosymmetry, I suppose)
With SAXS it should be easier to distinguish right-handed and left-handed
lock washers than it is to tell a right-handed from a left-handed wall
screw.
I use SUPCOMB from the ATSAS package to fit the Xtal structure to the SAXS
model. Then open this fitted file and your SAXS model again in pymol and you'll
see the fit.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Weifei
Chen
Sent: 26 June 2015 04:56
To:
Pramod,
You already got good suggestions on how to handle DNA contamination in protein
preparations.
Let me point out briefly that you haven't demonstrated yet that your
contamination is DNA.
I had the same observation when purifying UvsX. A very persistent and strong
contamination in all
Correction,
I meant to say 0.5kb, not 500kb
sorry for that.
S.
Dear all,
Sorry to disturb you.
I have install Phenix to my computer Centos 7.0.
When I want to use it I need to
cd /usr/local/phenix-1.9-1692/
and
. /usr/local/phenix-1.9-1692/phenix_env.sh
then type phenix in the command line every time.
I wish to use phenix in every terminate window and
Dear Weifei,
I am neither in the Phenix nor in the CCP4 teams so I let me remark that it
does not look reasonable, just a few minutes after Tom Terwilliger's mail :
I'll answer you on the Phenix BB as you've asked specific questions about
Phenix tools.
sending your mail (see below) asking
Yes, SAXS has an enantiomer problem - mirror image DAMMIN/F reconstructions
will give the same fit to the raw scattering data, whereas your protein
structure will only fit one hand.
SUPCOMB can certainly deal with this problem, as detailed in
I'd advise A LOT of caution here. If you're new to the technique, there are
several considerations to make well before you go docking a structure into a
reconstruction. Some suggestions:
1. Is your sample truly singular? BSA is a wonderful example of this
conundrum: at high enough
SASTBX has an online tool for achieving this:
http://sastbx.als.lbl.gov/cgi-bin/superpose.html
[image: David Briggs on about.me]
David Briggs
about.me/david_briggs
http://about.me/david_briggs
On 26 June 2015 at 11:39, Ashok Nayak ashokgocrac...@gmail.com wrote:
Dear Weifei,
It can also
Hi,
Follow up question on SAXS. Does SAXS have an enantiomer problem like electron
microscopy? In other words, does the calculated model possess the correct
handedness or can both handedness of a model fit the scattering profile just as
well?
Best wishes,
Reza
Reza Khayat, PhD
Assistant
Hi all,
I have SeMet data for which HySs locates 127 Selenium atoms with a CC of
0.31, which I think is decent.
Then I run Phaser to generate the first maps, and it gives a score of 25
and LLG of 190 or so...
The next step would be running Autobuild, however, the first models I
realize it is
Dear Weifei,
It can also be done manually in Pymol by changing the mouse mode from 3
button viewing to 3 button editing and later moving the envelope onto the
X-ray structure or vice-versa, however the best fit can be achieved in
SUPCOMB.
regards
Ashok Nayak
CSIR-CDRI, Lucknow
India
Hi Almudena,
I'll answer you on the Phenix BB as you've asked specific questions about
Phenix tools.
However in general it is a good idea to have a look at your map after phasing
and then the (usually two) maps after density modification. If they look like a
macromolecule then any of the
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