Hello,
Indeed, rigged positions do exist. In places where it is compulsory to
advertise positions but where the person who will get the job has been
selected in advance and is known already at the time the job
advertisement appears. This does happen in several countries worldwide.
I do not a
A conference on “*Structural Biology for the Bioeconomy: Infectious
Diseases and Biotechnology*” will be held at the *University of Cape Town*
from *1 December to 2012 to 4 December 2012*. The conference will
immediately precede the annual conference of the Microscopy Society of
Southern Africa (4
I think Fred is overstating the problem of compulsory adverts. There are
also cases where the expected "pre-selected" candidate does not get the
job as a better candidate appears. There are also cases where there is
eventually no job for anyone. Another outcome of an interview is you
don't get
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Kavya,
given the test is written in proper English with proper grammer etc.,
I think you are actually asking for censorship. I am happy ccp4bb does
not censor such emails, be they in accordance with one's opinion or not!
Best,
Tim
On 10/30/2012
Dear Sir,
I agree to that. But I presume that this is a platform to
discuss scientific problems and not a forum to discuss or
pour out personal frustrations. There may be other channels
for such grievances but not this. I was just hoping this does
not become a social network wherein everyone are f
Dear Kavya,
The CCP4BB is a closed community, in the sense that a user must subscribe
to the list before being able to post and that subscription requests are
handled manually rather than being granted by default. This is generally
sufficient to stop spam, irrelevant advertisements and blatant "tr
Dear all
Could we stop at this point.
regards
Garib
On 30 Oct 2012, at 18:35, Kavyashree Manjunath wrote:
> Dear Sir,
>
> I agree to that. But I presume that this is a platform to
> discuss scientific problems and not a forum to discuss or
> pour out personal frustrations. There may be oth
Dear Professor,
Thank you very much for suggestion.
With kind regards
B.Vijayakumar
On Mon, Oct 29, 2012 at 5:13 PM, Peter Keller wrote:
> Dear Tim and B. Vijay,
>
> On Mon, 2012-10-29 at 12:02 +0100, Tim Gruene wrote:
> > Dear B. Vijay,
> >
> > for single-wavelength (as opposed to Laue) X-ray
Read the manual? !!
There is a menu under
Other modelling tools" with a task - Add waters. That will scan the map and
add waters conservatively.
Or you can use the validation tool. Find difference map peaks, and decide
for yourseld whether they are waters. If you like the peak click Add atom
at poi
There is a big difference between reading "does not discriminate on the
basis of race, color, religion, sex, age, sexual orientation, marital
status, national origin, disability, or status as a disabled, Vietnam-era,
or other eligible veteran" and "below 35 years".
Then regarding Prof. Chitta's rep
Dear all, I have this (3.0 A) structure that has 8 molecules per ASU -
Phaser was able to find 7 molecules correctly, but not the last one, as
indicated by the .sol file (TFZ=5.1) below and the resultant density map. I
tried to delete the entry of the last molecule and give the truncated .sol
file
On Tue, Oct 30, 2012 at 7:44 AM, Jacob Wong wrote:
> Dear all, I have this (3.0 A) structure that has 8 molecules per ASU -
> Phaser was able to find 7 molecules correctly, but not the last one, as
> indicated by the .sol file (TFZ=5.1) below and the resultant density map. I
> tried to delete the
if you are sure about it's position, why not put the 8th molecule by hand?
why believe what a program does more than you can see by eye?
(this is nothing against Phaser, it is a great program)
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia -
Dear Coot-users,
I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package
was no problem at all it runs very smoothly.
However, whenever I want to save the coordinates the saving dialog open
-behind- the main window. To be more precise: the coordinate molecule
selector opens i
Are you sure that there are actually 8 molecules in the AU? I have on more than
one occasion calculated the expected number of protomers based on Matthews'
coefficient, only to find the solvent content is higher than I bargained for.
This thought is stimulated by the fact that the solvent conten
With permission from Nick Keep to forward to the bb which I am doing
right now :-)
If I may add: an organization advertising for a rigged job but not
reimbursing the candidate's expenses is, in my opinion, wrong doing. I
have never seen this happen in the UK but this has happened elsewhere...
Eike -
This unfortunately, is a well-known "feature" of coot on OS X - something to do
with Apple's implementation of X11.
Perhaps Paul knows if this happens on Mountain Lion, now that you need to use
Quartz X11?
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes G
Yes, it's still happening on Mountain Lion.
Cheers,
Ronnie
--
Dr. Ronnie Berntsson
PostDoctoral Fellow
Department of Biochemistry and Biophysics
Arrhenius Laboratories for Natural Sciences
Stockholm University
10691 Stockholm
Sweden
On Oct 30, 2012, at 16:51 , Antony Oliver wrote:
>
If you choose to use the excellent Mac OSX feature Exposé and Active screen
corners this becomes
less of a problem.
Damian Niegowski Ph.D.
Institute of Medical Biochemistry and Biophysics
Karolinska Institutet
Scheeles väg 2
171 77 STOCKHOLM
e-mail: damian.niegow...@ki.se
phone: 0046 8 5
I do not think "prof" Chitta Das understands the meaning of Equal
Employment Opportunity (EEO) in US. If Purdue which is an EEO institute had
followed the criteria of "below 35 years age" to select assistant profs
then he would not have served as an Assistant Prof today.
On Tue, Oct 30, 2012 at 5:
Hi,
At the risk of starting another series of rants, and somewhat off-topic, is
anyone actively using ResearchGate? It is bombarding me with email messages,
but I am uncertain as to whether people are really using it or whether it is
just scientific spam.
Hi all,
I'm working on a protein that I recently got crystals of. My functional studies
show that the protein has optimal activity at lower pHs, while losing >90%
activity at about pH8. I've been trying to soak/cocrystallize a substrate
analog (small molecule) into my crystals (grown at ~pH8) w
Dear Peter,
You could check your putative binding site to see if there are charged
groups which need to be protonated for your substrate analog to bind (or
whether the substrate analog needs to be protonated). In order to draw
physiologically relevant conclusions, you would need a crystal structur
Hello Adrian,
I use Research Gate and there are a few occasions where I have found
it useful, particularly the "questions" feature.
HTH,
Dave
David C. Briggs PhD
http://about.me/david_briggs
On 30 October 2012 16:13, Adrian Goldman wrote:
> Hi,
>
> At the risk of
I agree with Garib that we should stop this, because nothing productive seems
to be coming out of this discussion.
I however like to clarify one thing about the comment I made about agism. I
merely intended to interpret what the age limit preference means in the context
of Government of India's
Peter,
I think it would depend if the substrate analog have ionizable groups? If the
analog does not have ionizable groups, it is hard to imagine how the the
titration of ionizable groups on the protein would impair the binding.
Chitta
- Original Message -
From: "Peter Hsu"
To: CC
As for most questions in science, the answer is unfortunately "it depends."
A substrate analog may bind just peachy at a pH in which the enzyme is
inactive, depending on what interactions are involved in stabilizing the
analog compared to the substrate transition state. Such a complex may
stil
Dear CCP4bb users,
I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I
purified the protein in presence of Ca2+ and crystallized the Ca2+ bound
protein. I got crystal and solved the structure by SAD phasing at 2.1A
resolution. I can see the clear density in the difference
calculate an anomalous map, you should see the Zn signal even if you collected
at the SeMet peak.
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North
How would you distinguish between a mixture of Ca and Zn in the same locations?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kumar, Veerendra
[veerendra.ku...@uconn.edu]
Sent: Tuesday, October 30, 2012 1:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Su
On Tue, Oct 30, 2012 at 12:12 PM, Jim Pflugrath
wrote:
> How would you distinguish between a mixture of Ca and Zn in the same
> locations?
How often would they be likely to bind in the same place? Some of the
other transition metals are difficult to tell apart, but Ca and Zn
have very different
Dear Kumar,
If you build the sites as Ca2+, you can use a few things for validation:
- Ca2+ ions are exclusively coordinated by oxygens
- The bond valance method (implemented in e.g. WASP and WHAT_CHECK) can be
used to check whether a calcium ion makes sense. Do this before (reciprocal
space) refi
Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will
cycle through all the windows of the current program.
Jason.
--
Jason Busby
PhD Student
Laboratory of Structural Biology
School of Biological Sciences
University of Auckland
Thomas Building 110
3a Symonds St
Private Ba
On 10/30/12 15:02, Bosch, Juergen wrote:
calculate an anomalous map, you should see the Zn signal even if you
collected at the SeMet peak.
Jürgen
..
Ca can have a noticeable anomalous signal of its own, if your data are good.
If the possibility to collect new data exists,
If you calculate an edgeplot via Ethan's server:
http://skuld.bmsc.washington.edu/scatter/AS_form.html
you'll see that Zn @1Å has about 3 anomalous electrons whereas Ca less than 1,
so assuming occupancy of 1 the stronger anomalous signal should give you a
hint, second looking at the refined B-va
Do occupancy refinement. Especially if you use the new "anomalous
refinement" option available in refmac, phenix.refine and other packages
as well, you should be able to get a pretty reliable number for how many
"real electrons" as well as "anomalous electrons" are at each site. At
almost any
Chita,
I disagree that the age limitation for an entry level job does anything good to
a society. It gives a clear advantage to graduates from a few prestigious
universities, because less fortunate students would need more time to develop
their careers, no matter how talented they are. So, a com
Veerendra,
You can rule out if zinc has replaced calcium ions (although I agree with Nat
and others that looking at the coordination sphere should give a big clue) by
taking a few crystals, washing them a couple of times and subjecting them to
ICP-MS analysis, if you have access to this techni
This doesn't really give a useful answer. It tells you the overall
composition, but there is no means of knowing whether the metal ions are
equally present at all sites: some sites can favour Zn over Ca and vice versa.
Flame spectroscopy also works but has the same issue - and both have the
p
On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote:
> The coordination is indicative but not conclusive but, as I responded to the
> original poster, I think the best approach is to use anomalous scattering.
> You can measure just below and above the Ca edge,
Actually, you can't.
hi,
i have a large pdb file and i keep getting this error with refmac
ERROR: number of chains > 1500
i suspect something needs to be done to my pdb
any suggestions ?
thanks
jpd
hi,
answering my own question, but maybe this will
save some searching in the future,
the error was related to 3 letter RNA codes
refmac doesn't like that.
jpd
--- On Tue, 10/30/12, jp d wrote:
From: jp d
Subject: [ccp4bb] refmac
To: CCP4BB@JISCMAIL.AC.UK
Date: Tuesday, October 30, 2012, 3:43
Hi
Refmac use one letter code for RNA and two letter for DNA. Otherwise each
residue is considered as one chain (if there is no link between them).
I hope it helps.
regards
Garib
On 31 Oct 2012, at 08:05, jp d wrote:
>
> hi,
> answering my own question, but maybe this will
> save some sear
This paper describes use of data either side of the calcium edge:-
http://dx.doi.org/10.1107/S0907444905002556
This next paper describes a case of gallium and zinc mix at one site with
occupancy AND sigmas estimated with different software. This example is however
much better diffraction resolu
On Tuesday, 30 October 2012, Jrh wrote:
> This paper describes use of data either side of the calcium edge:-
>
> http://dx.doi.org/10.1107/S0907444905002556
I think that counts as "not amenable" (which is not quite the same
as "impossible". From the Methods section of that paper:
Measurements
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