Applications are invited for a postdoctoral position in my lab at the
University of Hawaii at Manoa, Honolulu, Hawaii, USA. Multiple
projects are available involving receptor tyrosine kinases, GPCRs,
structure based drug design, protein engineering, and developing
methods for membrane protein
Hi,
Just one correction to this. Phaser doesn't substitute values with the same
name in an output MTZ file. To get the anisotropy corrected F and SIGF values,
you have to run phaser in the separate anisotropy correction mode, and even
then it appends the string _ISO to the column names and
Applications are now open for the BCA/CCP4 Summer School in Protein
Crystallography to be held at Diamond (UK) from Tuesday 28th August to
Sunday 2nd September 2012. Applications close 1st May 2012.
The BCA/CCP4 Protein Crystallography Summer School is intended for students
and researchers
Hi all,
1)
I have a protein which gives two peaks on the 1ml Histrap column, Has
anyone seen this kind of behaviour and does this mean that there are two
populations of protein. They are partially seperated.
2)
I tried to load the two peaks seperately on the superdex-75pg column.
They came out as
Many thnaks for your input.
regards
Ros
On Wed, Feb 29, 2012 at 4:51 PM, Eleanor Dodson
eleanor.dod...@york.ac.ukwrote:
mtz(1) will contain h k l F SIGF I SIGI and optionally F+ SIGF+ and F-
SIGF- This is your master file, providing the space group is correct
It may NOT have the correct
Hello,
I run my model in Coot to do Temp Fact Variance Analysis.
There are red bars from the B-factor Variance graphy.
I click each red bar to exam the residues in Coot. Many of these residues
do not have the electronic density on their side chains, especially Lys
residues.
Here is my questions:
Ros,
I haven't used the Temp Fact Variance Analysis in Coot, but can guess
that the red bars indicate increased b-factor compared to the average of
your protein model?
If so, then:
*1. The lack of electronic density is the cause of these red-bars?*
Likely yes. If there is no density to support
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Hash: SHA1
Dear Ros,
yes, the lack of electron density is most likely the cause the these red
bars (unless you set the map level rather high, but at the default
chosen by coot that should be fine).
yes - if you don't see electron density you don't have
2. How do I fix them? delete the side chains?
Here we go again. Take a look at these threads
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
http://phenix-online.org/pipermail/phenixbb/2011-March/016875.html
--
Oh, suddenly throwing a giraffe into a volcano to make water is
Here we go again!
We neither have evidence that some mysterious side-chainnase has chopped
off all flexible surface side chains and in fact, at least I am pretty
sure these side chains are still there and moving around in the solvent
as indicated by their very/extremely high B-factors, which,
Hi,
You could try to lower the threshold used to contour the maps for these
side-chains (middle mouse button if you have a 3 button mouse with a
wheel in the middle). Quite often such side chains have lowish electron
density that does not appear at (say) 1.0 or 1.5 sigma (in the 2mFo-DFc
Typo (my fingers type faster than my brain...)
Original Message
Subject:RE: [ccp4bb] Temp Fact Variance Analysis
Date: Thu, 1 Mar 2012 14:56:06 +
From: Oganesyan, Vaheh oganesy...@medimmune.com
To: Vellieux Frederic frederic.velli...@ibs.fr
References:
Dear All:
Thank you very much for your comments.
I did not notice that this issue has been dicussed lately.
Thank you for your inputs
regards
Ros
On Thu, Mar 1, 2012 at 9:38 AM, Kelly Daughtry kddau...@bu.edu wrote:
Ros,
I haven't used the Temp Fact Variance Analysis in Coot, but can
On 01/03/12 14:26, Uma Ratu wrote:
Hello,
I run my model in Coot to do Temp Fact Variance Analysis.
There are red bars from the B-factor Variance graphy.
I click each red bar to exam the residues in Coot. Many of these
residues do not have the electronic density on their side chains,
Rashmi,
Has anyone
seen this kind of behaviour?
Yes, have seen differentially Glycosylated protein samples elute off
affinity resins as separate peaks.
but not that they behave different on gelfiltration like you described
in your case.
possible the samples interact with resin
Will there be
Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) has
launched a number of PDB archive browsers in the past two years. These allow
users to explore and analyse what is in the PDB based on concepts and
classifications they are familiar with, such as the EC
Hello all -
Short version: NCONT from CCP4 v6.2.0 doesn't properly recognize
comma-separated chain IDs with the source or target keyword.
I'm trying to use NCONT to determine contacts between antibody chains and their
bound epitope as part of a programmatic workflow. I'm using a Biopython
Hard to know for sure - I often set occ to 0.0, then redo refinement and
maps, only to find they have reappeared in the density at a low level.. In
the end all our models are defective - LYS and ARg and GLU etc often have
alternate conformations which we cant model at low resolution, and the
Thanks to Pius for the tip that I can use more than one source keyword.
ncont xyzin my.pdb eof
source L
source H
target P
eof
works like a charm!
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 329/398
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On
Dear CCp4ers,
A good morning to everyone.
Today, I have a structure that I initially refined in space group P6522,
1mol/asu.
Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma 3
2.61-2.55A: Rsym=39.6%, I/sigma 10
50.00-6.13: Rsym=6.4%
Some mild anisotropy in the resolution limits is
Hi Wolfram,
a few points:
- R-factors in twin refinement vs non-twin refinement are not directly
comparable:
G.N. Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261
http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf
- did you make sure free-R flags assigned having
I'm worried when you say that you use the initial job's output MTZ. Refmac
replaces F with a detwinned F in the output file so you wouldn't be refining
against your measured data in the subsequent round.
Best wishes
Randy Read
Randy J. Read
On 2 Mar 2012, at 02:00, wtempel
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