try out the search - it
is a catalytic quartet of residues - a superset of the catalytic triad.
Regards
Tom Oldfield, PDBe.
HEADERHYDROLASE (SERINE PROTEINASE) 22-JAN-85 5CHA
5CHA 3
COMPNDALPHA CHYMOTRYPSIN A (E.C.3.4.21.1)
5CHA 4
SOURCECOW
imension. Is there a
simpler way to do this, am I over thinking the problem?
This was helpful
http://en.wikipedia.org/wiki/User:Vossman/3D_Line_Regression
<http://en.wikipedia.org/wiki/User:Vossman/3D_Line_Regression> but I'm
still struggling
Thanks,
Grant
--
Tom Oldfield
Hi
If any use: I have commonly used the C/C++ and Java threaded code to create
parallel processes. Python threading is badly implemented and best avoided,
use sub-processes instead as these are forked.
1) CPU intensive code with no dependency scales close to N where N <
cores available,
for al
Katherine
I am not exactly sure what sort of tool you would like to use, but there are
a couple of options found here...
http://www.ebi.ac.uk/pdbe-as/pdbetemplate/
The last option DB search
http://www.ebi.ac.uk/pdbe-as/pdbesearch/
allows you upload a fragment of structure - a small number of r
atlas
page
to check that this correct. You can also [Get] a list of entries as
text or XML,
or put the SQL into the query browser to fine tune this.
Regards
Tom Oldfield
Check with PISA@EBI, it has database searches where you can fetch all
dodecamers in the PDB
Eugene
On 20 Feb 2013, at
data representation.
Regards
Tom Oldfield
Dear all,
Could you please teach me any method to present the relationship
between resolution and B values of all the x-ray structures in Protein
Data Bank. Can the PDB statistics in RCSB do it?
Thank you very much!
Q. Cai
No virus found in this mes
Hi
In you post you say you want to fit a small number of points. Note
that the
original algorithm of Kabsch has a number of maths pathalogical conditions
where points have symmetry or lie in a plane/line - this is common for
a small number of points (fitting residues or your example).
The ma
Hi
I would just like to note that a web-browser plug in is on the client
machine - to
view a PDB file in any viewer like this (ie Astex-viewer, jmol) requires
that file to be physically
downloaded onto the client computer - and put into the TEMP folder of
that machine.
As such, the act of vi
Shya
There have been a number of issues of the releases of the JVM, particularly
with browser IE9 - most resulting in security exceptions when accessing
data files.
You should be able to update your Java on your computer as these problems
appear to have been finally resolved through the normal
not sure if this is suitable.
Regards
Tom Oldfield
Dear all,
I would like to know what program/software you usually use to plot the 2D
interactions between ligand and protein. As far as I know, LigPlot is powerful
but need some skills. Also a web-based program from PDB server is easy to use
but
Some important reason for using 64bit is due to the following.
The "effective" precision of a float (32bit) is about 5 dp
The "effective" precision of a double/real*8 (64 bit) is about 10 dp
The number of dp is only approximate since we are encoding this using
binary.
The max/min value of a f
this has effected your work.
We are have identified and fixed the problem and are currently testing
the change and should have the fix in production by the end of the week.
Regards
Tom Oldfield
PDBe
Dear CCP4bb,
We are trying to get some detailed interface information from an
Robert Immormino
Does this service answer you question. It is limited to 10,000 return
results for the statistical analysis so it is possible to ask general
questions
where the statistics are truncated.
http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatisticsAtom.jsp
Tom Oldfield
Hi
Rakesh
Looking at the
http://www.pdbe.org/statistics
Structure Statistics
Then for all structures a we see that Rdiff of > 0.7 is not that uncommon
with this about 1 sigma away from the mean value of 0.4 for all structutures
and 0.45 for your resolution range
For structures with Rdiff ra
Yuan SHANG
1) DIY
The way that has been used is to calculate the inertia tensor matrix for
helix (or
any other secondary structure element). You can chose backbone atoms or
just
the CA atoms. Then calculate the eigen vectors and values from this and
the largest
eigen vector will be the best
tal : Rdiff from the Experiment drop down
and resolution for the second parameter drop down.
[show Distribution] will then produce a dynamic rotatable graph that
can be selected to determine subsets.
Regards
Tom Oldfield
PDBe
> Dear all,
> I remember that there used to be a post about th
-wise to deposit
the structure in the current state of refinement as there is clearly an
issue.
Regards
Tom Oldfield
Hi Sampath,
this is how the distribution of Rwork, Rfree and Rfree-Rwork look like
for 'all' PDB structures refined at around 2A resolution. The "<<<
Tom Oldfield
Does anyone already have the PDB-wide R/Rfree gap versus resolution data
(it does not seem that the PDB maintains one)?
Ed.
The friendly people in Uppsala has something here by the name Harry
Plotter: http://xray.bmc.uu.se/gerard/supmat/eds/plotter.html
This might be somewhat
With respect to water structure in Xtal structures.
I have studied water "order" (or should that be sensibility) within
xtal structures by studying water shell statistics. It is possible to
divide xtal structures into 2 camps. The first show some sensible
water shell structure that correlates t
19 matches
Mail list logo
