Two things for Coot users...
Firstly, I have just uplaoded the remaining Linux binaries for Coot 0.6,
i.e. Fedora 8, Fedora 10 and Ubuntu 6.06 (with python and gtk2 gui).
You can find them on the Coot website here:
http://www.biop.ox.ac.uk/coot/software/binaries/releases/
Secondly, please c
Well - cad cant work with that script so somehow it is being generated
wrongly, presumanly in Arp/warp stage..
It would need input such as:
LABIN FILE 1 E1=FBshasol E2 = something - presumably SIGFBshasol
Eleanor
Narayanan Ramasubbu wrote:
Hi:
Sorry for the same posting in here as well b
The 2nd peak is a shoulder of the origin peak at 1.0 0 0 so should be
ignored..
The 3rd peak is 16% of the origin - rather marginal I would say. So I
dont think there is clear evidence of translational NCS
Eleanor
Sylvia Fanucchi wrote:
Morning all
Apologies for the simple question.
Hi,
This question may have been asked before, so please excuse me for re-posting
it. I notice that when I do a round of 10 cycles of refmac combined with
(5cycles, 3 sigma level, 1.4 A resolution) of findwaters in coot, some water
molecules from the different coot cycles fall one on top of the
A funded postdoctoral position is availableimmediately in Weill Cornell Medical
College in New York City. The research focus will be on
thecrystallography-based study of the structure and function of membrane
transporters.The laboratory is fully equipped and has regular access to
crystallizati
Dear Colleagues:
This is a reminder that today is the deadline for Early Registration and
Abstract Submission for the 2010 Symposium on Structural Analysis of
Supramolecular Assemblies by Hybrid Methods. The Symposium will be held at
Granlibakken Conference Center, Lake Tahoe, California, and t
Hi, All,
I have a general question for refinement. I tried to refine a dataset that
is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77,
RMS(bonds): 0.003
however, when I check with molprobity, There are still some outliers and
some bad contact that is overlap > 0.4 A.
Hi,
the exact answer to your question is here:
http://cci.lbl.gov/~afonine/for_ak/validation.pdf
In particular, your question below is spelled out is discussed staring
from slide #2.
Pavel.
On 12/14/09 7:50 AM, rui wrote:
Hi, All,
I have a general question for refinement. I tried to refi
A less exact answer, albeit less precise and informative than the very
nice PDF and the very useful Polygon ideas, is:
"very well done, but have another look at this couple of Ramachandran
outliers and also consider loosening up the geometry a bit".
;-)
A.
On Dec 14, 2009, at 17:04, Pavel
hypFdemo_28.pdb:
CRYST1 58.351 58.351 155.876 90.00 90.00 120.00 R 3 2 :H 1
I dont hold a candle for either of these SGs but Phaser is now
outputting the R 3 2 :H and many many other CCP4 programs are then
falling over
Can the symlib be modified to accept both?
Eleanor
--
CALL FOR PROPOSALS FOR BEAMTIME WITH ONLINE MICROSPEC
*Proposal Deadline 13th of January 2010*
There will be beamtime available at the ESRF for MX data collection with
a setup that allows online monitoring of UV/VIS spectral changes of the
This is pointed out (in absolutely unobvious way - I wish I can add
voice to that PDF) at the slide #19 -:)
(except loosening weights).
P.
On 12/14/09 8:35 AM, Anastassis Perrakis wrote:
A less exact answer, albeit less precise and informative than the very
nice PDF and the very useful Polyg
Course Announcement
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We are pleased to announce our practical course " Scientific Programming and
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Disclaimer: Phaser is the greatest MR program I've ever seen.
However:
"The Hermann-Mauguin space group symbol is given without parenthesis,
e.g., P 21 21 2 and using the full symbol, e.g., C 1 2 1 instead of C
2."
-- The RCSB
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
I don'
I have a 10-residue stretch of a protein that adopts an interesting
conformation; I'd like to know if this conformation occurs in other
proteins. I'd welcome suggestions for tools that will allow me to to
search for this peptide conformation in the PDB.
I naturally thought of DALI, but it s
I believe that Coot also outputs R 3 2 :H (Paul can clarify).
We need some standardization on the hexagonal setting for R32. Having
just suffered through a fairly brutal structure determination in this
space group, I can say that there are some 'issues' with this. For
instance HKL outputs a lin
Postdoctoral position in structural studies of membrane proteins by electron
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A postdoctoral position is available in the School of Biology at the Georgia
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Mon, Dec. 14th 2009
London
Hello,
I think you can you SSM
Secondary Structure Matching
at PDBe
http://www.ebi.ac.uk/msd-srv/ssm/
you can upload your coordinate file
and try to match to the whole of PDB.
Hope it helps
Miri
On Mon, 14 Dec 2009, Patrick Loll wrote:
I have a 10-residue stret
Hi Stephen,
> R32
> H32
> R32 :H
Correct. These are all hexagonal setting. As far as I know, the
hexagonal setting of R32 (R32:H) is the first one that comes up in the
ITvA as is listed a R32. The rhombohedral/primitive setting of R32
(R32:R) comes second in the ITvA, I guess the first setting ta
Thanks Peter. The unfortunate thing is that not all of the programs are
able to understand these different notations, and that they
preferentially use different ones. It would be nice if we all agreed to
standardize. I, personally, have no problem with R 3 2 :H since that is
what it really is.
On Thu, 10 Dec 2009 13:06:36 -0600, Tanner, John J.
wrote:
>Some of you might be curious about the "Ajees et al debacle" that Jacob
mentioned in his message. Here are two links:
>
>Nature Brief Communication that questioned the validity of one of Murthy's
structures:
>
>http://www.nature.com/na
Fellow users,
I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the
following problem when I try to run ccp4i for the first time as root to
configure the program:
r...@:/home//Documents# ccp4i
No protocol specified
Application initialization failed: couldn't con
Stuart,
Are you logged-in as root or are you working in a root shell ( using su
or sudo)? Depending on your security settings X-windows may not permit
a program that is run from a root shell to access the display, which
belongs to the user logged-in through X-windows.
I get around the administra
With 'sudo' you should not have this issue.
I agree, though, that having a separate user account to install
crystallographic programs is quite an advantage from an administrative
point of view.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID =
I was running from a root shell. Ubuntu does not let me login as root. That
is normally a good thing, but if I remember correctly to finish the ccp4i setup
last time I on a CentOS system I had to login as root. I will try to reinstall
tomorrow using sudo, but frankly I hate using it.
Stuart
Mark A. White wrote:
Stuart,
Are you logged-in as root or are you working in a root shell ( using su
or sudo)? Depending on your security settings X-windows may not permit a
program that is run from a root shell to access the display, which
belongs to the user logged-in through X-windows.
Anot
On Mon, 14 Dec 2009, Edward A. Berry wrote:
Mark A. White wrote:
Stuart,
Are you logged-in as root or are you working in a root shell ( using su
or sudo)? Depending on your security settings X-windows may not permit a
program that is run from a root shell to access the display, which
belongs t
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