Dear Meg,
There is a database of refolding conditions from which you could get some
inspiration.
http://refold.med.monash.edu.au/search.php
The Urea conditions I have seen there mostly use 37C. for
solubilization/refolding and nearly all contain a reducing agent. Have a
look. There are also a gr
Hi,
Thanks to all for kind replies
I got my output using PHENIX
phenix.xtriage filename.sca residues=no.of residues
and again thanks Peter Zwart
On Wed, Dec 2, 2009 at 12:57 PM, Pankaj Chauhan wrote:
> Hi ,
> In one of my 60mer structure at 3.5 A, , when I run methews in ccp4i, it
> does
At 10:35 PM -0600 12/2/09, Dima Klenchin wrote:
2. Chances are good that you can use as high temperature as you need
to dissolve. I've come across protocols using >=65C in the presence
of 100 mM bME to ensure complete unfolding of the polypeptide and
reduction of disulfides (seems essential fo
We use 8M urea solubilization buffer for our protein in inclusion bodies
and recommended temperature is 10-15C. but in 8M conc the urea does not
dissolve and is in crystalline form only, will it have any effect on
solubilzation efficiency. Our solubilization time is 1 Hr and after that
we centr
Hi all,
We use 8M urea solubilization buffer for our protein in inclusion bodies and
recommended temperature is 10-15ยบ C. but in 8M conc the urea does not
dissolve and is in crystalline form only, will it have any effect on
solubilzation efficiency. Our solubilization time is 1 Hr and after that w
Hi,
you can do similar thing (that is resulting in similar outcome) in
phenix.refine by increasing the weight on ADP restraints term. Example:
increase "wu" or decrease "wxu_scale". Although I believe a regular
refinement of individual isotropic ADPs should normally work just fine
at 3A resol
James,
> nearBragg2D does not contain a random number generator. I made the atom
> constellations for my DS calculations using an awk script.
My point was that your 'constellation of points' has to be some kind of random
sampling since it has to be a sampling both over the lattice and over tim
Ian,
nearBragg2D does not contain a random number generator. I made the atom
constellations for my DS calculations using an awk script. I would
appreciate it if you could create a constellation of atoms that has the
"correlated displacements" you are talking about, so that I (and others)
ca
> "important". The
> answer to the last question appears to be "never". The
> "background"-subtracted spot intensities really are the square of the
> Fourier transform of the AVERAGE electron density in a unit
> cell. Yes,
> the arithmetic average. Does not matter where the background come
I recently wrote a little jiffy program for calculating "general
scattering" images that could perhaps be useful for answering some of
the questions raised on this thread:
http://bl831.als.lbl.gov/~jamesh/nearBragg/nearBragg2D.c
Instructions for compiling and running are in this text file:
http
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Dear all,
First, I am happy that there is am easy solution.
Second, let me clarify that ARP/wARP CCP4i GUI uses standard CCP4i
library functions to read in files etc etc.
I am sorry to get technical, but what I do is simply:
CreateInputFileLine line \ [...lines deleted...]
-setfile
IMHO this is a bad idea as the restraints can give undue weight to poorly
ordered residues in order to favour the tighter distribution that you are
specifying.
I have found bindividual.inp to perform at low resolution reasonably well, and
I think it is more realistic than group B-factors. The
Dear Colleagues,
Further discussions of this most interesting topic have continued between
Colin and myself off-line. Not least we have basically ended up assembling a
references list for further reading! One such I need to check and my copy of
the relevant book has required me to get a replacement
Yes, matthews_coef has a limit of 48. You need to change:
PARAMETER (MAXMOL=48)
in $CPROG/matthews_coef.f and recompile. Ask if you need help with
this.
So looks like its time to increase the parameter in line with the
capabilities of computers and crystallographers
BTW matthews won't t
Dear Bulletin Board,
I received this information from Axel Bruenger, who rightly corrected me on the
modification to be made to the bindividual.inp file:
>As an fyi, the sigmas should be made smaller to get a narrower B-factor
>differences.
My previous post:
> You modify the file bindividual.
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