Hi all,
Thanks for providing the solution.
Regards,
ARKO
On Wed, Feb 22, 2012 at 10:14 AM, arka chakraborty <
arko.chakrabort...@gmail.com> wrote:
> Hi all ,
>
> I will like to know which program we can use to calculate R-mergd-F( not
> Rmerge) between two data sets, or more generally R factor
Why not just use PROCHECK program?
在 2012年2月22日 下午6:24，Thomas Holder 写道：
> Hi Dialing,
>
> if you know some python you can use PyMOL.
>
> # get C-alpha b-factors as list
> from pymol import cmd, stored
> stored.bfactors = []
> cmd.iterate('name CA', 'stored.bfactors.append((b,resv))')
>
> # min/m
> You might get lucky by setting up crystallization plates, but chances are
you won't get very useful information from them, especially if your
aggregated protein is soluble.
I seem to fail to understand how crystallization plates would give
information in the not-special case of protein aggregate
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If you haven't done so already, I would screen buffer conditions
(pH, salt concentration, glycerol, strongly reducing conditions,
ligands, detergents) by DLS to see if you can reduce aggregation. You
might get lucky by setting up crystallization plates, but chances are
you won't get very usefu
hi
did u have other crystals grew in different conditions in your additive screen ?
in my case, i did the additve screen for the condition i got twinned crystals
i got crystals grew in few conditions
one of them is salt but it still gave me twinned crystals
then i tried NDSB-221 and the crystals
Dear all,
Thanks for your response to my quarry about surface residue mutation. I
tried the SERp Server, but did not get satisfactory clue. This software
classified our protein as difficult to crystallize, however we have
crystallized and solved the structure also. But our crystal form is not
good
Although this is not the answer to your question,
Bryan Matthews papers show
In T4 lysozyme A mutation at A73 to AAA is shown to make extensive
core-repacking in T4lysozyme that makes the
enzyme inactive.
Is the issue here is to use lysozyme for bacterial cell breakage while
your fusion
protein rem
This was meant to Raji,
So here it goes to all.
-- Forwarded message --
From: Zhang, Zhen
Date: Wed, Feb 22, 2012 at 12:15 PM
Subject: RE: [ccp4bb] Aggregated protein for crystallization
To: Pius Padayatti
Hi Pius,
I have done exactly that. I have one protein eluted at void
Dear Theresa,
all types of twinning - merohedral, pseudo-merohedral and non-merohedral
ones - can be solved given somewhat favorable conditions. In small
molecule crystallography, it's quite common, especially for (pseudo)
merohedral twins, it becomes increasingly popular for macromolecules as
Dear All,
We are working with proteins with a lot of surface hydrophobicity and
hence solubility is a big issue. We so far have tried expressing them as fusion
proteins.The strategy has yielded soluble protein but most of the protein
elutes in the void volume on a gel-filtration colum.
Hi all.
I have a 'learning' question based on recent thread where crystal twinning is
mentioned. With the current computational methods, what types of twinnig can
and cannot be solved with computers?
Thank you.
Theresa
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I read your description of the crystals and Figure 4 of the following paper
came to mind. Post-crystallization treatment in lower PEG eventually allowed
them to tease the bundles apart.
1. MacRae, I. J. & Doudna, J. A. An unusual case of pseudo-merohedral
twinning in orthorhombic crysta
Forgot to mention, that this 2.5-3A diffracting crystal was the same one that I
have been unable to index and suspect are twinned due to the presence of these
other fused crystals in the same drop.
Thanks for any input.
Dear All,
We have an open position at Genentech in the Structural Biology group for
an Associate/Senior Associate in our protein purification and
crystallization laboratory (Job #: 380684). Prior experience in
purification and/or crystallization is required. Preference will be given
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some more thoughts,
Do a cryo-EM imaging, it will be ideal than DLS.
if the particle sizes are uniform i would think your protein in that state
might be useful.
cheers
Padayatti
On Tue, Feb 21, 2012 at 6:21 PM, Raji Edayathumangalam
wrote:
> Hi Folks,
>
> As crazy as it sounds, if you have crysta
One of our sister CCPs, CCPBioSim, is running a one-day workshop on "How
to set up a Protein Simulation" on April 20th in Cambridge. It is aimed
at people new to biological molecular dynamics simulations, and may be
suitable for any crystallographers who want to have a go. It will use
the (free) MD
If you have tried all of the other things suggested by others (especially
beam-center and direction of rotation), you can try the keyword 'weak level' in
indexing box (see page 29 on HKL manual
http://hkl-xray.com/sites/default/files/manual_online.pdf or
http://www.hkl-xray.com/denzo-keywords-
Dear Sreetama,
ProFit (http://www.bioinf.org.uk/software/profit/) does the RMS-by-residue
calculation for multiple chain superposition.
Avinash Punekar
Hi Vijay,
The obvious person to answer this is Phil Evans, but he
is in New Zealand at the moment and may well not be reading Emails, so
you might need to wait until he is back in the UK (1-2 weeks). I know
that he felt the POSTREF option was not an important one to maintain,
Hi all,
Does anyone have version(s) of scala and postref that "work together
in tandem" and willing to share. Even older versions of these programs
are fine with me.
I can not seem to make the recent versions of the programs work
together... even though there is a POSTREF option available
Hi Dialing,
if you know some python you can use PyMOL.
# get C-alpha b-factors as list
from pymol import cmd, stored
stored.bfactors = []
cmd.iterate('name CA', 'stored.bfactors.append((b,resv))')
# min/max b-factors with residue number
print min(stored.bfactors)
print max(stored.bfactors)
# d
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Jacob,
you may also like one of the many google hits with "mencoder add subtitles".
Tim
On 02/21/2012 04:59 PM, Jacob Keller wrote:
> Dear Crystallographers,
>
> is there a good way to put text labels into movies from pymol or
> otherwise? It
Dear Raji
Running a blue-native gel with lanes in the presence and absence of a reducing
agent could prove quite informative. DLS could also return a quick result on
the particle distribution in your sample. In that case I would measure samples
as fractionated from the superdex200 and compare th
Not sure if it will be helpful... but my protein is not the most
stable protein, in fact, it does aggregate over time (most likely due
to its 'sticky' nature).
However, I still get crystals. The problem is the crystals are among
the gunks and precipitates.
Your case might be different si
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