hello,everybody . due to excess nucleation,I often get many tiny crystals
instead of few,large crystals.i wana optimize the condition, does anyone
have adivce about this?
Best regards.
Dear zq deng,
The standard method, I dare say, in such a case is micro seeding:
reduce the precipitant to a concentration so that you just do not get crystals
any more, wait until the drop equilibrates (about one day in the case your
precipitant is a salt, up to 5-7 days for high MW PEGs),
then
Dear Zq,
A few ideas:
1) Vary protein concentration, temperature, or protein : mother liquor ratio.
2) Try dioxane - it is supposed to reduce nucleation.
3) give your protein a good hard spin before you set up drops to remove
aggregates.
4) seeded factorial screen.
5) re-purify on gel
... only in the [0kl] plane. ...
I'm sure you've already checked, but if during data collection the [0kl]
axis was nearly perpendicular to the rotation axis, then you may only have
to superimpose (with ipdisp) few suitably selected images to obtain a
small (low resolution) portion of what you
Dear Zq CCP4BB readers,The precipitant is the main component that affects nucleation.In specific cases other factors can be used to modulate nucleation as mentioned before by others: protein concentration, temperature, drop size, initial protein/precipitant ratio etc. All good components of a
All -
No doubt this topic has come up before on the BB: I'd like to ask
about the current capabilities of the various integration programs (in
practice we use only MOSFLM XDS) for reading compressed diffraction
images from synchrotrons. AFAICS XDS has limited support for reading
compressed
d*TREK will process compressed images with the following extensions: .gz
.bz2 .Z .pck and .cbf
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian
Tickle
Sent: Thursday, May 06, 2010 6:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Processing
Hi all,
the problem for Zalman monitor to newer MACs etc. is :
From Zalman (
j...@zalman.co.kr ) I got this Mail:
I
can provide the fix – a custom DVI cable specifically for the ZM-M220W.
It
resolves the issue of the swapped pins 15 16 of the ZM-M220W,
which is not
an issue with older
Entering xds gzip at www.ixquick.com came up with
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html:
To save space it is allowed to compress the images by using the UNIX compress,
gzip, or bzip2 routines. On data processing XDS will automatically recognize and
expand the
Jim, thanks for the info. At present we use d*TREK mostly only for
in-house data (Saturn, Jupiter R-axis) so the data collection rate
is much lower and in any case we would gain nothing by compressing
them since the I/O is the same whether it's gzip reading in the images
or d*TREK. Our problem
Hi Ian
I've looked briefly at implementing gunzip in Mosflm in the past, but never
really pursued it. It could probably be done when I have some free time, but
who knows when that will be? gzip'ing one of my standard test sets gives around
a 40-50% reduction in size, bzip2 ~60-70%. The speed
Hi Tim thanks for that, sorry yes I missed that page. But I'm still
not clear: is it uncompressing to disk or is it doing it in memory? I
assume the latter: if the former then obviously nothing is gained.
You're right about the compression factor, it's more like a factor of
2 or 3, I should have
Hi Harry
Thanks for the info. Speed of compression is not an issue I think
since compression backing up of the images are done asynchronously
with data collection, and currently backing up easily keeps up, so I
think compression straight to the backup disk would too. As you saw
from my reply
Dear Zq Deng,
I've had success with the dilution method as described
by Dunlop and Hazes: http://scripts.iucr.org/cgi-bin/paper?en5016
For me it worked for a couple of projects, and gives you a bit more to
permutate than just varying the protein:mother liquor ratios, as Thomas
Compression methods such as gzip are unlikely to be optimum for diffraction
images, and AFAIK the methods in CBF are better (I think Jim Pflugrath did some
races a long time ago, and I guess others have too). There is no reason for
data acquisition software ever to write uncompressed images
I mistakenly sent this off to Enrico, rather than to the CCP4BB. Apologies to
Enrico.
Begin forwarded message:
From: Charles W. Carter, Jr car...@med.unc.edu
Date: May 6, 2010 6:50:23 AM EDT
To: est...@cea.fr
Subject: Re: [ccp4bb] control of nucleation
In fact, there is quite good
The results from compressing a diffraction image must vary quite a bit on a
case by case basis.
I looked into it a long time ago using images from a few datasets from 2
different projects. Compress was quite faster than gzip or bzip2 in these
tests. It also delivered the less compression. gzip
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As part of the structure annotation process, wwPDB members provide
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these documents will be available from all wwPDB
Hi
I have succeeded by using oil (such as parafin oil ... etc ) at reservoir on
top of the reservoir solution. You have to try several trials to find optimum
ratio.
With regards
Syed
--- On Thu, 5/6/10, zq deng dengzq1...@gmail.com wrote:
From: zq deng dengzq1...@gmail.com
Subject:
Hi Greg,
If you want manual control over user-defined restraints, which I've found
helpful when dealing with low-resolution structures, ResDe might help. You
can define restraints in PyMol and then save the restraint file in the
refmac format. I hope if helps. Here is the link:
yet another compressor to consider : xz
http://tukaani.org/xz/
hth
Something I have been playing with recently that might address your
problem in a way you like is SquashFS:
http://squashfs.sourceforge.net/
SquashFS is a read-only compressed file system. It uses gzip --best,
which is comparable to bzip2 for diffraction images (in my experience).
Basically,
Does anyone know of a program designed to both store information on functional
motifs in proteins, as described in the literature, and to retrieve such motifs
within a given protein sequence?
Rex Palmer
Birkbeck College
Sorry for the off topic question but since Aquifex aeolicus is a favorite of
many structural biologists I wonder if anybody can point me to a reliable
source for DNA from this critter (or any other Aquifex). ATTC does not seem to
have it...
Thanks in advance
Marcelo
actually,the protein grow in too different condition.both have excess
necleation,and one condition is that just puting protein in the drop and not
mixing with the precipitants.there is one another problem how to
cryo-protect.
2010/5/6 syed ibrahim b_syed_ibra...@yahoo.com
Hi
I have succeeded
Ian Tickle wrote:
I found an old e-mail from James Holton where he suggested lossy
compression for diffraction images (as long as it didn't change the
F's significantly!) - I'm not sure whether anything came of that!
Well, yes, something did come of this But I don't think Gerard
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