To reply to the original question, can the calculated Matthews coefficient be
wrong?:
have you read the paper by Matthews? There is a distribution of solvent content
in macromolecular (protein)
crystals. It has a peak and tails on both sides. Meaning that there are
outliers in the
Dear Xinghua,
the solvent content provided by yhe Matthews-program is certainly correct.
Whether or not it applies to you protein is a different issue. With only 2
molecules in the asymmetric unit the solvent content rises to 65%, and this is
stll perfectly fine for proteins. So carry out
Dear Garib,
I tried both methods as you advised, but they didn't work for me yet.
1. I ran refmac with the option residues are close only and included the
keyword file which has the line MAKE CHECK NONE as recommended in the log
file. However, the refinement was still aborted. It seems that
Dear all,
I think we all think that macromolecular structures are the best there
is... And now we have a chance to prove it to the world.
The Scientist is organizing a competition to elect the best website.
One of the competitors is the Proteopedia web site
(http://www.proteopedia.org).
Hello,
I am not a crystallographer, so I will ask
a maybe stupid question.
When you say After molecular replacement you should check the result
with the model building program of your choice and correct as many
errors as possible before running a refinement program.
Can this step be automated
Hi,
No such thing as a stupid question. If the resolution is sufficient,
arp_warp does a good job. But it is a reconstruction and REFINEMENT
program. But checking the proper packing (that there are indeed contacts
in the 3 dimensions of space to form the crystal): takes only 10 seconds
using
Vellieux Frederic wrote:
Hi,
No such thing as a stupid question. If the resolution is sufficient,
arp_warp does a good job. But it is a reconstruction and REFINEMENT
program. But checking the proper packing (that there are indeed contacts
in the 3 dimensions of space to form the crystal):
On Fri, Jun 25, 2010 at 12:41 AM, Francois Berenger beren...@riken.jpwrote:
When you say After molecular replacement you should check the result
with the model building program of your choice and correct as many
errors as possible before running a refinement program.
Can this step be
Dear All,
a quick question about Ranom. In articles and textbooks it is usually
reported that:
Ranom = Sum |Mn(I+) - Mn(I-)| / Sum ((Mn(I+) + Mn(I-))/2),
while in the output log file of scala it is reported that:
Ranom = Sum |Mn(I+) - Mn(I-)| / Sum (Mn(I+) + Mn(I-))
i.e. the factor 2 is
Buccaneer 1.5 is available from here:
http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html
The new version doesn't have any new model building features, but
incorporates significant new features to automate tidying up of the
resulting model, as follows:
- Model tidying: Chain
Forgot to also post this response to the BB.
Randy
Begin forwarded message:
From: Randy Read rj...@cam.ac.uk
Date: 25 June 2010 12:59:12 GMT+01:00
To: Yong Y Wang wang_yon...@lilly.com
Subject: Re: [ccp4bb] error in running Phaser NMA mode
Dear Yong,
Sorry about that! I suspect the
Please respond to Joseph Curtis (joseph.cur...@nist.gov) and Susan Krueger
(susan.krue...@nist.gov ) if you are interested.
=-=-
Here is the link.
NIST-ARRA Fellowship Program
http://www.nistfellows.umd.edu/index.htm
If there is someone that is interested then they should
Dear Xinghua,
Of course, you can have 2 molecules in the asu. However, if things don't
it is worth to double-check your space group or check for twinning.
Cheers
christian
xinghua qin wrote:
hi CCPeers
The Matthews coefficient of my protein is 3 calculated with
matthews-cell content
Dear all,
Is there an image indexing program that assigns and shows the Miller
indices onto the image itself, or maybe can read the indexing matrix to
point these indeces onto the image for inspection? I tried to use LABELIT,
but it showed the integrated Bragg spots as circles without the
Hi CCP4ers,
I am looking for an affordable UV microscope (not used for automation). I
would appreciate it if you would like to share your experience.
Thank you,
Lei
Dear Marco,
I'm not sure exactly what you want (for example do you want the
indices of ALL reflections to be shown or just individual ones)
but iMosflm (CCP4 package) may be able to do what you want.
After indexing the image, the predicted reflections will be displayed (as
boxes). If
I have (probably) all issues of Physics Today unbound
from 1983 through 2010. Any takers?
Postage reimbursement is expected.
Frances Bernstein
=
Bernstein + Sons
* * Information Systems
It is out of principle misleading to think of the Matthews coefficient as one
hard number. Xinghua mentions it actually: 'with 87 % confidence' (although
'confidence as in confidence interval' is a statistically too hard term here
imho). The Matthews probability calculator gives a more complete
Hi ALL
I don't know if I'm asking the right question:
What are Remote, Inflection and peak values for X ray data collection?
Sorry if question is wrong or under-status.
thanks in advance to all
--
best regards
Sudhir Kumar
Research Scholar
Structural Biology Laboratory
SLS, JNU,
New Delhi-110067
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