The sizes of several arrays (such as the ones that store atomic positions) are
defined at compile time, and your structure appears to have run up against one
such limit. Here's what the CNS website says:
"Changing array dimensions
The array dimensions for several arrays which may need to be cha
Hi Eleanore,
On Tue, Aug 21, 2007 at 12:56:40PM +0100, Eleanor Dodson wrote:
> 5) The need for crystallographic education for readers and students
Just discovered SciVee (YouTube for scientists) at
http://www.scivee.tv/
which is operated in partnership with the Public Library of Science
(PLo
Hi all,
Great idea! As being relatively new to the field, I definitely find
this idea appealing. Actually hearing the talks would indeed be quite
educational.
Cheers,
Ronnie Berntsson
On Aug 23, 2007, at 10:57 AM, Clemens Vonrhein wrote:
Hi Eleanore,
On Tue, Aug 21, 2007 at 12:56:40PM
Dear group members,
I would like to bring following the openings to your attention:
ANNOUNCEMENT TITLE: Postdoctoral positions in crystallography in
Stockholm, Sweden
DEADLINE FOR APPLICATIONS: 25 October 2007
TYPE OF POSITION: Post-Doc(s)
INSTITUTION/DEPARTMENT: Center for Infectious Medicine, De
Mischa,
I don't think that the field of nanotechnology crumbled when allegations
against Jan Hendrik Schon (21 papers withdrawn, 15 in Science/Nature)
turned out to be true. I don't think that nobody trusts biologists
anymore because of Eric Poehlman (17 falsified grants, 10 papers with
fa
Dear colleagues,
1) I think Ajees et al. should make available the raw diffraction images of
the structure in paper that has caused so much literary commotion, unless
they haven't already done so. Perhaps simply put them in an open ftp server?
As I imagine, unless I have missed something, these
Hi Shivesh
I had something like this recently and found that changing the pH stopped
the precipitation and the size of the crystals improved. If the crystals
are large enough even if there is ppt present I would still try and
collect data on them. This is likely not the case for you or you wouldn
Hi,
I'm a evolution/genetics grad student trying to address protein
questions. I'd like to figure out the easiest way to extract contact
density (and possibly higher order contact traces in the future) from
PDB files or SCOP domains. I'm wondering if there is a server or a
list somewher
Shivesh,
You also might be precipitating out a contaminant, aggregate, isoform,
etc., and its removal from the solution allows crystallization of the
other.
Lisa
-Original Message-
From: CCP4 bulletin board on behalf of Rob Gruninger
Sent: Thu 8/23/2007 10:30 AM
To: CCP4BB@JISCMAIL.AC.UK
I 100% agree with Jordi Benach. However, the problem with idea is that
it requires the real images in question to exist. I am willing to take any bet
that they will never be shown to the public.*
Jordi Benach wrote:
Dear colleagues,
1) I think Ajees et al. should make available the raw diffract
Sorry for the repost, but I think my question got lost in the earlier
thread.
I've found
$CCP4/x-windows/ipdisp/src/pack_c.c, pack_f.f and so forth, but they
apparently don't build by default, and when I try to, I get
You need to make mosflm-bits in the library for the image-packing stuff
On 23 Aug 2007, at 18:17, Zbyszek Otwinowski wrote:
I 100% agree with Jordi Benach. However, the problem with idea is that
it requires the real images in question to exist. I am willing to
take any bet
that they will never be shown to the public.*
Since by taking bets, one simply prefers on
James Holton wrote:
How MUCH do you want to bet?
;)
Any amount, as long as we are taking about real diffraction images
corresponding to the deposited file with "observed" structure factors.
I doubt that simulated diffraction images will be shown, because they
are easy to be recognized as such
On Thu, 23 Aug 2007 10:46:51 -0700 James Holton <[EMAIL PROTECTED]>
wrote:
>
> So would PNG be better? It does support 16 bit greyscale. Then
> again, so does TIFF, and Mar already uses that. Why don't they use
> the LZW compression feature of TIFF?
Because of the patents on LZW
(http://en.wi
How MUCH do you want to bet?
;)
-James Holton
MAD Scientist
Anastassis Perrakis wrote:
On 23 Aug 2007, at 18:17, Zbyszek Otwinowski wrote:
I 100% agree with Jordi Benach. However, the problem with idea is that
it requires the real images in question to exist. I am willing to
take any bet
Well, I know it's not the definitive source of anything, but the
wikipedia entry on JPEG2000 says:
"The PNG (Portable Network Graphics) format is still more
space-efficient in the case of images with many pixels of the same
color, and supports special compression features that JPEG 2000 does not
Hi Bill,
> It seems it would be good to have available if we are all going to
> put our images on our web-servers.
Probably easier to either just bzip2 the images (which works reasonably well
but is somewhat slow) or use one of the imgCIF "jiffy" programs to do this,
which will correctly retai
Dear all
I welcome all the suggestions regarding my crystals which is coming with the
precipitation.The pI of the protein is 4.2 and the drop precipitates with
MPD as low as 30% within 4-5 hrs.I am trying the pH ranging from 3.6-5.2 at
16C.There is no precipitation at 20% of MPD.Also,at high conc,t
Sorry - this may have been mentioned previously, but have you tried banging in
some glycerol (5-10%)?
J
shivesh kumar <[EMAIL PROTECTED]> wrote:>
> Dear all
> I welcome all the suggestions regarding my crystals which is coming with
> the
> precipitation.The pI of the protein is 4.2 and the drop
I agree to this last suggestion. For one of my protein, I had to add at
least 10 % of glycerol in my buffers to keep my protein stable while
purifying. For crystallization, I diluted it to 20 % glycerol (vapour
diffusion method) which allowed it to be stable in the crystallization
drop and eventu
Thanks, Graeme.
Is there any advantage to bzip2-ing the individual images rather than making
one bzip2-ed tarball with tar cvfj?
Bill
On Thu, 23 Aug 2007 20:12:26 +0100
"Winter, G (Graeme)" <[EMAIL PROTECTED]> wrote:
Hi Bill,
> It seems it would be good to have available if w
Is there any advantage to bzip2-ing the individual images rather than
making one bzip2-ed tarball with tar cvfj?
Yes. If you have folks sending you images by sftp or e-mail, then you
don't have ensure a tarball of Giga or Tera bytes works. You can send the
smaller multiple files and restart
Hello All,
I have a question about some data with which I have been grappling. The crystal
appears to be primitive cubic(p23). Are there alternate ways to index cubic
data? I ask this question without regard to anomalous data. I have looked at
several datasets in Xtriage. I wanted to merge data
I've been reading the contributions on this topic with much interest.
It's been very timely in that I've been giving 3rd year u/g lectures
on protein X-ray structures and their validation over the past week.
As part of the preparation for the lectures, I searched the PDB for
structures with hi
Green, Todd wrote:
> Hello All,
>
> I have a question about some data with which I have been grappling. The
> crystal appears to be primitive cubic(p23). Are there alternate ways to
> index cubic data? I ask this question without regard to anomalous data.
For overall indexing, there are two ways
Hi all,
Great idea! As being reasonably new to the field, I would definitely
welcome those videos. Not that I don't read Acta D papers, but it is
always nice to hear the talks directly, and would certainly be quite
educational.
Cheers,
Ronnie Berntsson
--
Ph.D. Student
Department
In the cases you list, it is clearly recognized that the fault lies
with the investigator and not the method. In most of the cases where
serious problems have been identified in published models the authors
have stonewalled by saying that the method failed them.
"The methods of crystallogr
- Original Message -
From: "Jenny Martin" <[EMAIL PROTECTED]>
To:
Sent: Thursday, August 23, 2007 5:46 PM
Subject: Re: [ccp4bb] The importance of USING our validation tools
My question is, how could crystals with 80% or more solvent diffract so
well? The best of the three is 1.9A reso
Another example of a structure with intervening
layers of weak electron density at 1.75 A
resolution is Pb2+ bound calmodulin that Mark Wilson
solved in my laboratory: M.A. Wilson and A.T. Brunger, /
Acta Cryst./D59, 1782-1792 (2003), PDB ID 1NOY.
The intervening layers are not entirely disor
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