Thank You all for your warm responses.
The issue now has been resolved. The co-ordinate which pop up in the error
box were not matching to the PDB text co-ordinates.So we have gone through
the placed water molecules one by one in PBD text file and checked for the
same co-ordinates. We could find
Dear all,
I am currently recruiting for a Research Assistant/PhD position in my lab at
Newcastle. The project involves studying the molecular basis of chromosome
synapsis and genetic exchange during mammalian meiosis, principally through
X-ray crystallography and biophysics. I am looking for a
Hi all, recruitment plug for Diamond:
The Data Acquisition (GDA) group at Diamond develop the software
interfaces that many of you use a lot, if you collect your diffraction
data there -- so presumably many of you have strong opinions about it,
or indeed visionary ideas for what it could and
Dear all,
I was wondering if there are 3D monitors for X-ray crystallography other
than Zalman.
Thanks
Fares
--
Dr. Fares Z. Najar
Research Faculty/Adjunct Professor
Department of Chemistry and Biochemistry
Stephenson Life Sciences and Research Center
101 Stephenson Parkway
Norman, OK 73019
ASUS VG278HE Black 27 2ms (GTG) HDMI Widescreen LED Backlight LCD Monitor 300
cd/m2 50,000,000:1 Built-in Speakers 3D ready, Height, Swivel adjustable
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fares Z.
Najar
Sent: Thursday, September 04,
Hi, All CCP4BB Users,
I have quite some data sets(~15) collected at different beam intensities,
the individual dataset can diffract to ~3.8 A @I/dI=2. If I combine them,
with AIMLESS in CCP4, the resolution can be extended to ~3A@I/dI=2. But,
the Rmerge or Rpim is way high, in 10s or even 100s.
It seems as though this topic is re-visited quite often on this discussion
board. I would refer you to search the CCP4BB archives
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/ for an extensive
amount of discussion on this topic over the past couple of years.
A quick synopsis of an
On 04/09/14 19:06, Lie Ma wrote:
Hello all,
I am trying to make a model of an oligosaccharide which contains several sugar
monomers. I obtained the monomers from coot library and put them into the
electron density. But I don't know how to make covalent bond between these
monomers.
If you
Dear Charles,
I would ignore (high resolution) R-values for justifying the rsolution
cut-off. If you are talkig about 100s %, I have published data with
Rmeas 500% in the highest resolution shell.
You are quite save cutting the resolution where I/sigI = 2.0, by todays
knowledge this is actually
CASP11: Critical Assessment of Structure Prediction
Date: December 7-10, 2014
Venue: Paraiso Lindo, Puerto Juarez, Riviera Maya, Mexico
Connecting Airport: Cancun, Mexico
The CASP meetings focus on assessing the state-of-the-art in protein structure
modeling. Results of the 11th blind structure
David, Thanks for providing your data. my CC1/2 is often about 0.6, 0.7
since I cut at I/sigmaI =2.
Tim, you are right. I am conservative on this since I am still a new comer
in this field.
Charles
On Thu, Sep 4, 2014 at 2:36 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Dear Charles,
I
Hi all,
I am just curious whether there are some tools extracting the Euler angles
from a fractional coordinate matrix. I have no luck searching it online.
Alternatively, I found the analytical solution for the Euler angles from an
orthogonal coordinate matrix. So in the worst case, my problem
I am sorry, just to clarify, the fractional coordinate matrix I referred to
is a rotational matrix in the fractional coordinate system.
On Thu, Sep 4, 2014 at 3:52 PM, Chen Zhao c.z...@yale.edu wrote:
Hi all,
I am just curious whether there are some tools extracting the Euler angles
from a
On Thu, Sep 4, 2014 at 4:05 PM, CPMAS Chen cpmas...@gmail.com wrote:
Do you guys have some recommendation of the criteria? phenix reported
anomalous measurability, CCP4/aimless has RCRanom. Sometimes, they are not
consistent.
The measurability isn't always useful - it's definitely correlated
Dear Charles,
I usually look at the course of CC1/2 (anom) across the resolution bins.
It should be high'ish at low resolution and a good resolution cut-off
for e.g. shelxd is where it drops below 30%.
The certainly by far best criteria is a traced structure (for a protein,
though). With shelx
The orthogonal/fractional matrix is outlined here:
http://www.iucr.org/__data/assets/pdf_file/0009/7011/19_06_cowtan_coordinate_frames.pdf
Sorry to say I apparently ditched my old Fortran o2f and f2o programs to
do that.
Bear in mind, however, that orthogonal has no fixed orientation with
Also, if you process your data using XDS, it'll give you good indication for the strength of the anomalous signal. I find the XDS and Aimless indications to agree quite well.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Thank you, Paul.
And do I need to provide additional cif file which describe the bond?
Leo
On Sep 4, 2014, at 2:23 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
On 04/09/14 19:06, Lie Ma wrote:
Hello all,
I am trying to make a model of an oligosaccharide which contains several
sugar
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