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
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
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
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
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 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
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,
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
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
Link to the advertisement:
http://chemistry.ucsc.edu/~wgscott/temp/RNAad.pdf
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
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
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