HI,
You could use the LINK command after going through Jligand for your modified residues. There is a very nice tutorial here:
http://www.ysbl.york.ac.uk/mxstat/JLigand/
in case you haven't done this before.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of
Have you checked the dictionary cif calls them L-peptide?
Eleanor
The header should look like this..
# data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code
_chem_comp.name _chem_comp.group _chem_comp.number_atoms_all
_chem_comp.number_atoms_nh _chem_comp.desc_level ALA ALA
In new version (it should be in ccp4 6.2.0, if not then it will come ccp4 6.3,
otherwise you can take it from York's web site: ) TPO as well as SEP are
peptides.
Break in coot may be due to misinterpretation of SEP or TPO as peptide in coot
and it may be because of older version of the
Dear All,
We have collected a data for a protein crystal at SER-CAT Chicago and the
detector is mar300.We are using mosflm to process the data.While indexing, the
beamstop which it is taking is wrong, due to which it fails.
I am trying to define the beamstop manually using tools like mask and
Dear All,
Thanks for the suggestions. I will work on them.I had not worked on the
modified residues, so thanks for all the valuable suggestions.
RegardsRajesh
Date: Thu, 22 Mar 2012 10:15:55 +
From: ga...@mrc-lmb.cam.ac.uk
Subject: Re: [ccp4bb] refining phosphorylated residues
To:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear,
as you open the imosflm-GUI there are three editable fields on top
underneath the top menu which are for the beam position (x,y in mm) and
the detector distance.
As you tell imosflm which images to use, a display window pops open
which allows
Dear Sonali,
Just to add to Tim's reply, when you open the image with
iMosflm, you can Drag and drop the direct beam position in the
image display window. First, you have to click on the leftmost
icon in the row of icons under the image filename (a green
cross) which will display the
If you are lucky (or should I say unlucky) and have an ice-ring on the same
image or on another image collected during the same shift and similar distance,
you can estimate the beam centre using the fit circle option.
Although software (and beamlines) have improved greatly, it can still be a
Postdoctoral position,
Institut
de Biologie Stucturale, Grenoble, France
A two year
postdoctoral position for a biochemist/structural biologist is
available in the Synchrotron Group at the Institute for
Structural Biology (IBS) in Grenoble
Dear all,
I am trying to express a eukatiotic protein (E. coli codon optimized sequence)
with a GST tag at the N-terminus. I always get my overexpressed protein and a
contaminant around 60kDa. This contaminant is not washed out of the column when
washing glutathione beads with 1M NaCl-buffer.
Dear Andrew and all the people for their help,
I am providing mosflm the right beamstop and now, I am able to do the indexing,
refinement and indexing too.Then I run scala for the output mtz file and it
shows Rmerge too high 0.58and also when examining the spots and predictions in
the image, it
What resolution are you working at? What are the unit cell dimensions?
On Mar 22, 2012, at 11:10 AM, sonali dhindwal wrote:
Dear Andrew and all the people for their help,
I am providing mosflm the right beamstop and now, I am able to do the
indexing, refinement and indexing too.
Then I
I would hazard a guess of Gro-EL.
With regards,
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ
email:
Announcement of a working group for the adoption of the PDBx/mmCIF format
for deposition and as an exchange format between programs for
macromolecular crystallography.
Following a meeting at PDBe Hinxton on 26/27 September 2011 organized by
the wwPDB it was decided to form a working group for
Hi Maria,
As mentioned by Tony, it could be a chaperonin. Having little of ATP (0.5mM
or less) and Mg2+ (1mM) in lysis buffer might help.
Good Luck,
Partha
2012/3/22 SANCHEZ BARRENA, MARIA JOSE xmj...@iqfr.csic.es
Dear all,
I am trying to express a eukatiotic protein (E. coli codon
Is any NMR blog available for discussion?
Amit Luthra, Ph.D.
Post-Doctoral Fellow
The Radolf Laboratory
Department of Medicine
University of Connecticut Health Center
[e] aut...@uchc.edumailto:aut...@uchc.edu
[p] 860/ 679 - 8390
[w] http://spirocheteresearch.uchc.edu/
Hi Sonali,
How did you assign the spacegroup ... did you run POINTLESS ?
A table of Rmerge vs resln from SCALA would be helpful in addition to a
screen shot of an image as Francis suggested.
Andrew
Dear Andrew and all the people for their help,
I am providing mosflm the right
The imminent replacement of Mobile-Me by iCloud provides an impetus for me to
upgrade to Lion; but I'm currently happily using old-school stereo (i.e., a CRT
monitor + Crystal-Eyes LCD glasses) under Snow Leopard. Can anyone attest to
being able to use such equipment with Coot/PyMol under LIon?
You can check the following site.
http://qa.nmrwiki.org/
http://nmrwiki.org/wiki/index.php?title=Blogs
+--+
Cho, Min-Kyu
Postdoctoral scholar
Dept. of Biochemistry (Sanders lab.)
Vanderbilt University School of Medicine, Nashville, TN
Phone: 615-936-3757
|
Amit,
One resource being developed is the NorthEast Structural Genomics Consortium
( http://www.nesg.org/ ) NMR Wiki.
Please check it out at http://www.nmr2.buffalo.edu/nesg.wiki/Main_Page.
Michael A. Kennedy, PhD
Eminent Scholar and Professor
Department of Chemistry and Biochemistry
Miami
Dear All,
This is the second announcement of an EMBO Practical Course
on the Structural Characterization of Macromolecular Complexes.
WHEN: 4-9 June 2012
WHERE: Grenoble, France
TOPICS INCLUDE:
Expression purification of multi-subunit complexes
Biophysical biochemical
*Dear CCP4
*
*Please forward this advertisement to suitable candidates*
*best Preben
*
*
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership,
University of Oslo*
**
*1 PhD research fellowship*
*Background:*
The Centre for Molecular Medicine Norway (NCMM,
Dear CCP4bb members
I have a 3.0 Å dataset which has an off-origin peak of height 36% in patterson
map. The peak is at fractional co-ordinates 0, 0.5, 0.5. Data has been indexed
in P2(1)22(1) SG using HKL2000. I have located all the molecules in asu (as
far as I know) using Molrep with the
Dear All,
Sorry for the non-ccp4 topic. I am trying make my Baculovirus
preparation less time consuming and I found this paper:
http://www.ncbi.nlm.nih.gov/pubmed/15939308
Time reduction and process optimization of the baculovirus expression
system for more efficient recombinant protein
http://www.lablife.org/p?a=vdb_viewid=g2.XyCli.11qhPxFTK4WFNANgFD.Xc-
Is this that you were looking for?(all thanks to google)
lablife gives you the whole sequence. make it if you really need it.
All the best.
Padayatti PS
On Thu, Mar 22, 2012 at 8:39 PM, Nian Huang huangn...@gmail.com wrote:
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