In fact, I would put it even stronger, if we know a referee is being dishonest,
it is our duty to make sure he is removed from science, blacklisted from the
journal etc.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
Glycerol is known to be able to reduce nucleation. This might be countered
by an increase in protein concentration.
Vera, L., Czarny, B., Georgiadis, D., Dive, V., Stura, E.A. (2011)
Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des.
11: 2755–2762.
Enrico.
On Tue, 03
Hi James,
My previous message on this matter remains unnoticed, but I also suggested a
very simple solution to the data fraud: the crystallographers should submit to
PDB partially processed data, like unmerged partial reflections. These files
are much smaller than the images, and only a few
Yes, Rajesh, I completely agree with Pius. There is absolutely nothing wrong
in asking a question on ccp4bb.
The suggestion 'read a book and search on-line information sources' is a good
one on any subject.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
Dear Colleagues,
One thing that would help is avoiding misappropriated priority of
research
results would be to join the math and physics community in their robust
use of open-access
preprints in arXiv. Such public preprints establish reliable timelines
for research credit
and help to
Florian Schmitzberger wrote:
Dear Toby,
I don't think there is a basic problem using glycerol in
crystallization. Glycerol will affect the vapour pressure (if it is not
present in the well/precipitant solution) and 10 % glycerol is ~ 1.3
molar concentration. During equilibration the drops may
The time has come for me to upgrade my Linux OS to something more recent
for me and my student workstations. A 32-bit distro is certainly
conservative and compatible with CCP4 and Coot, but it seems like that
solution hobbles my hardware and puts some limitations on available
memory, even with
We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine
on this.
I can't say I notice a big performance boost from the 64 bit side of things.
Maybe I'm just impatient.
cheers, tom
Tom Peat
Biophysics Group
CSIRO, CMSE
343 Royal Parade
Parkville, VIC, 3052
+613 9662
I agree with Herbert that a pre-print setup is one way to establish priority
and get useful comments for an author.
And I know this has been discussed before, but another way is to remove the
anonymous aspect of the review, as this would achieve the same as the community
pre-print distribution
Whatever you do, make sure you have enough bottled water before the next
doomsday:
http://en.wikipedia.org/wiki/Year_2038_problem
I am using 64-bit linux almost exclusively for some time now. XRD
software works fine, no lingering issues that I can report. ia32-libs
do the trick for 32-bit
On the topic of MX fraud : could not an encryption algorithm be
applied to answer the question of truth or falsity of a pdb/wwpdb/pdbe
entry? has anyone proposed such an idea before?
for example (admittedly this is a mess):
* a detector parameter - perhaps the serial number - is used as a
public
I have RHEL62-64 in a win 7-64 8GB desktop VMware installation. CCP4, ccp4i,
coot, and shelxcde beta executables run fine.
There were issues with the coot package installation due to unresolved
dependencies
and my ignorance thereof, but I think a working RHEL62-64 compatible package
is available
Dear Colleagues,
on behalf of the selection committee I'd like to draw your attention to the
the Trueblood award:
http://www.amercrystalassn.org/content/pages/main-award-descriptions
This will next be awarded in 2013, however nominations are sought now so that
the winner can be
When superimposing 2 structures in coot, I get a core rmsd in the output.
What does this mean? Which residues are included in the core rmsd? Are
these all the residues that have equivalent residues in the moving and
reference molecule?
Yrsyla
--
Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
We have been using 64 bit Linux for several years. I'm not aware of any
lingering issues with the 64 bit-ness.
Linux is always sprinkling in a few new bugs, but I don't know of any
current issues with 32 bit vs. 64 bit.
On 04/03/12 15:57, Roger Rowlett wrote:
The time has come for me to
I'm not sure how encryption can solve a problem of truth or falsity.
Public key encryption only says that the message that is decrypted using
the public key must have been encrypted by someone who knows the private
key. A person can use their private key to encrypt a lie as well as the
truth.
Hi Roger
CCP4 and Mosflm work fine in my testing - I do builds for Linux and
Macs, both 32 and 64 bits. I wouldn't expect to see a difference in
performance (and don't see anything significant in practice).
One thing - I think you will need to install 32-bit compatibility
libraries for
Fedora and RHEL 64-bit work well and run pretty much all
the standard programs (CCP4/Coot/Phenix/CNS/SHELX). By
installing the relevant 32-bit libraries you can also run
older programs if need be.
On a related note, XtalView will work on Fedora/RHEL if
you install/compile the appropriate
Dear Colleagues,
We would like to point out that the application deadline for the 5th annual
CCP4 Summer School From data collection to structure refinement and beyond is
April 17, 2012. The school will take place from June 19 through June 26, 2012
at the Advanced Photon Source (APS) near
Dear All,
Here may be another example for the importance of image storage.
http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html
Regards,
Kevin
On Tue, Apr 3, 2012 at 5:16 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote:
I'm not sure how encryption can solve a problem of truth or falsity.
AFAIU any given checksum will tell you if a file is corrupted or not.
My brain decided to interpret that as true or false. and
A person can
Roger,
My lab is using 64 bit distros of SUSE and Linux Mint and hasn't had
any compatibility issues that I can recall.
Ho
Ho Leung Ng
University of Hawaii at Manoa
Assistant Professor, Department of Chemistry
h...@hawaii.edu
Date:Tue, 3 Apr 2012 15:57:40 -0400
From:Roger Rowlett
Hi Rajesh,
Have you looked at how well conserved these Cys/His residues are? Is the
spacing similar to known zinc fingers? Might be good things to consider if you
suspect a zinc finger in your protein, of course you probably know this already.
Best,
Peter
Orcus,
if you put yourself persistently into the face of guys who play hard, you
need to learn to
take a few hits and shake it off. Maybe a little retrospection on why your
postings might
perhaps possibly maybe perceived as somewhat self-promoting and ungracious
could be helpful.
The
Hi,
If it is under a UNIX-like system, I would probably make a new user for myself,
say, projects_2012, etc.. It is not perfect, but it is a simple solution.
Zhijie
From: wtempel
Sent: Tuesday, April 03, 2012 9:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ccp4i project display
Dear
Thanks of your education. I got it.
By the way, what does Orcus mean here?
Regards,
Kevin
On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.)
hofkristall...@gmail.com wrote:
Orcus,
** **
if you put yourself persistently into the face of guys who play hard, you
need
Trollus maximus perhaps ? But it could have different meanings e.g. in German
there is something going south if it went down the orcus :-)
Don't worry to much and relax.
Jürgen
On Apr 3, 2012, at 8:22 PM, Kevin Jin wrote:
Thanks of your education. I got it.
By the way, what does Orcus mean
Might I suggest looking to Sean Seaver and the P212121.com as an example of
a a successful crystallographer science blogger though the site has shifted
more towards a consumable supplier in recent years.
I would also consider looking into adding an RSS feed to your site so that
those people
My intent with the troll joke was to give a humorous reminder that a little
self promotion is ok, but a couple times a day is annoying. Orcus means troll,
as in Internet troll, meaning one who subverts the intended use of the site and
is annoying people. You have made a number of on topic posts
Hi,
Regarding the online image file storage issue, I just googled cloud storage
and had a look at the current pricing of such services. To my surprise, some
companies are offering unlimited storage for as low as $5 a month. So that's
$600 for 10 years. I am afraid that these companies will
Hi All
I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt
60 and 8 Kda respectively.
Molecular repalcement (60Kda protein as template) with Phaser gave a
solution with 6 molecules in ASU.
A continuous density is also obersved near two different chains which i
consider as
Hi Intekhab,
With 6 copies of the complex in ASU, NCS averaging might give you a better map.
Uppsala software factory has everything you need to do that:
http://xray.bmc.uu.se/usf/. Check the RAVE package. Particularly, have a look
at the average.csh script listed in the RAVE package page in
On Apr 3, 2012, at 7:19 PM, Katherine Sippel wrote:
I would also consider looking into adding an RSS feed to your site so that
those people interested in your articles can be informed without spamming the
boards.
Why continue to punish him? Adding an RSS feed means installing and
James makes an important point. I've come to regret my joke as showing poor
manners. I hesitate to add to more email that no one cares about, but I do
think it is important to contribute the idea that the positive tone of this
forum needs to be protected. I apologize, and suggest my comments
As already suggested you should use NCS averaging, but I would go the Parrot
way http://www.ccp4.ac.uk/html/parrot.html or DM using a mask for your monomer
of the hexamer and first ignoring the peptide. Do you have a ring or a dimer of
trimers ?
If however your two peptides follow NCS as well
Ok Kevin,
thank you for your response. You got it, and that is good, and I am sure
we'll hear from you again and that is
good too. But let me explain the Orcus (however, keep in mind, I am only a
single contributor and almost
always do not represent the majority of CCP4BB users' opinions.
The sad situation is that more and more scientists are becoming
desperate (for funding or tenure or both) and are told 'publish or
perish'; they become obsessed with impact factors, sensationalise the
data in the process (be it complete fabrication or 'massaging' the
results) and rush to
If journals would require that not only coordinates, but also structure factors
would be made publicly available immediately AFTER publication, any sloppy
author will be caught within days by the Rups, redo people and Bricognes.
Anyone who would then still submit and publish questionable data
Dear all,
My question is related to a sample preparation.
I’m working with a complex that can be stabilized with glycerol (at least
10%) during purification. The use of detergents does not help. After
purification, the sample is homogeneous (EM) and can be concentrated
(3-4mg.mL-1) . I already
I think that to review a paper containing a structure derived from
crystallographic data should indeed involve the referee having access
to coordinates and to the electron density. Without this access it
is not possible to judge the quality and very often even the
soundness of statements in the
Dear colleagues,
likely some of you have experienced that with 100s of ccp4i projects, the
menu (limited to 25 lines?) exceeds the horizontal limitations of the
computer display. Are there any suggestions how to handle this many
projects? Added difficulty: I expect that were I to eliminate
Hi
I was thinking about the last statement in the Acta editorial - It is
important to note, however, that in neither of these cases was a single frame
of data collected. Not one.. This brought me back to the images..
To date there is no global acceptance that original diffractiom images
Hi Fred,
I'll go public on this one. This happened to me. I will not reveal who reviewed
my paper and which paper it was only that your naive assumption might not
always be correct. I have learned my lesson and exclude people with overlapping
interests (even though they actually might be the
The remedy for the fact that some reviewers act unethically is not withholding
coordinates and structure factors, but a more active role for the authors to
denounce these possible violations and more effective investigations by the
journals whose reviewers are suspected by the authors of
Dear All,
I am trying to crystallize a protein, so far I got no diffraction though I have
large crystals.It has few cystines and a histidine near by at N-terminal. I
dont have much literature on biochemistry of this protein available in pubmed
(5 papers only).Is there a way if I could check
Read a book.
If you can't find a book then ask the all knowing Google.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh
kumar
Sent: Tuesday, April 03, 2012 10:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] zinc fingre
Dear All,
I am trying to crystallize a
Thanks.. I will.
Date: Tue, 3 Apr 2012 15:17:34 +
From: debas...@uab.edu
Subject: Re: [ccp4bb] zinc fingre
To: CCP4BB@JISCMAIL.AC.UK
Read a book.
If you can’t find a book then ask the all knowing Google.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
On Behalf
There are review articles on various motifs. I think that I remember
that you can also find motifs via sequence or structure classes on
places like SWISSPROT/EXPASY. A quick search of PUBMED did not
produce a single-source paper listing the various motifs...and there
are several. Biochemistry
Dear Toby,
I don't think there is a basic problem using glycerol in
crystallization. Glycerol will affect the vapour pressure (if it is
not present in the well/precipitant solution) and 10 % glycerol is ~
1.3 molar concentration. During equilibration the drops may increase
in volume,
When this happens there is usually a serious problem with the data.
Have you checked the truncate output for a non-cryst translation vector? It
would look as though you have something which is generating a pseudo
translation along x of ~ 0.2
Look at the hklview pictures of your data and see
Hi Rajesh,
First of all you did the right thing to ask people here about our doubts.
There is nothing wrong in asking questions.
The board is for asking questions realted to crystallography
(all aspects).
Padayatti
On Tue, Apr 3, 2012 at 11:07 AM, Rajesh kumar ccp4...@hotmail.com wrote:
Dear
We use ethylene glycol and glycerol mainly to reduce nucleation (or showering
of crystals). However, we also found that these two additives may not be
interchangeable, that is effects of these reagents were markedly different on
crystallization behavior of a particular protein.
Debasish
This is a final reminder that the Canadian Macromolecular Crystallography
Facility (CMCF) is accepting applications for an intensive 5-day hands-on
synchrotron data collection school at the Canadian Light Source (CLS) in
Saskatoon. The School will take place June 5 - 9, 2012. Participants will
Mark,
I know some stories (which of course I'll not post here) from the
Crystallography field and from other fields where reviewers profit from the
fact that suddenly they have new, interpreted data which fits very well
with their own results. Stories like to block a manuscript or ask for more
I don't agree, if we know a referee is dishonest we should try and ruin his
whole career, not just prevent him from scooping us in this one case.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel.
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