Dear CCP4ers:
Does anyone know an existing program to calculate the lateral
displacement---the vertical offset, measured as a fraction of the
the heptad repeat---of neighboring helices in coiled coils or helix
bundles, either parallel or antiparallel?
Your input is greatly appreciated.
Have a n
Link to the advertisement:
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The Department of Molecular, Cell and Developmental Biology at the
University of California, Santa Cruz invites
applications for a tenure-track faculty position. We seek candidates
whose research centers on fundam
Dear All,
I have a structure to 1.65A crystallized in high sulphate conditions.
The R factors went smoothly to 21% and 23% (Rfree), but the
difference map shows positive difference peaks in otherwise normal
regions of the main chain and is more noisy than expected in general.
Since the el
Try the CASTp site at http://sts.bioengr.uic.edu/castp/calculation.php
Anthony
Anthony Addlagatta, PhD
Institute of Molecular Biology
University of Oregon
Eugene, OR-97403
Phone: (541) 346-5867
Fax: (541)346-5870
Web: http://uoregon.edu/~anthony
On Aug 3, 200
Hi Xiaofei,
You might want to try the backrub tool in KiNG
(http://kinemage.biochem.duke.edu/software/king.php) .
This allows one to make subtle correlated changed along the mainchain,
and watch the effect on the fit to the Ramachandran plot.
Richardson Lab
Duke University
On 8/3/07, Xiaofei J
Every modern structure should be "above average" by procheck criteria.
For modest resolution structures, the availability of ncs restraints
should have a big effect on one's Ramachandran expectations: I've
found ncs restraints at 3-3.5A do wonders for the Ramachandran plot
even when they don't
Dear Enrique,
VOIDOO does what you want. http://xray.bmc.uu.se/usf/voidoo_man.html
Other similar programs are CAVENV in the CCP4 suite, and CAVER
(http://loschmidt.chemi.muni.cz/caver/), which finds tunnels, and gives you
tunnel radii.
best wishes
James
Dr. James Murray
Biochemistry Buildi
Dear all,
I am now preparing my structure for deposition. The
crystal diffracts to 3.0 A. R: 0.20; R free: 0.25.
What I am concerned with is the Ramachandran plot;
83.5% in core region, 15.8% in allowed, 0.5 % in
general allowed,0.2% in disallowed region. The model
fits in density pretty well an
Procheck puts out such a correlation (% most favorable
vs resolution) in the _04.ps file. For example look at
page 7, first panel of the sample procheck output at:
http://sb20.lbl.gov/SQR/procheck-2H88.pdf
It appears that 83.5% would be well above average
for a 3 A structure according to procheck
Dear All,
I am wondering if you know a program to calculate the volume of a particular
crevice in a PDB we are analysing.
Thank you in advance!
Enrique
For dealing wih PDBv3.0 format, our lab has two new facilities to
offer:
MolProbity, our structure validation and improvement webserver
(http://molprobity.biochem.duke.edu/ ), now accepts coordinate files
in
either PDBv2.3 or PDBv3.0 format and uses the latter for computations.
A formal descri
using
http://www.ebi.ac.uk/msd-srv/msdsite/
and then under "Ligand environment:"
click Edit and draw the interaction
The oval shape is a ligand - click on it
and say make it GAL
you can say add a TRP connected to a ligand
(it is a rectangle shape)
and click on the "bond" circle and
Try submitting your coordinates to www.ebi.ac.uk/ msd and choose the
task MSDpisa
It gives you lots of info including that..
Eleanor
Sreeram Mahesh wrote:
Hi All!
I have found stacking interaction between aromatic residues of a
structure of an enzyme. does anybody knows any server which
MAPMAN from Uppsala will do this. Adam
On Thu, 2 Aug 2007, Bernhard Rupp wrote:
> Dear All -
>
> before I code ahead - is there a simple program/script available where I can
> read
> in a map and it gives me a basic 1d density histogram (or the tabular
> data at least) in return?
>
> Thx, br
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