Dear Guangyu,
80% solvent is an awful lot. The first thing I would do is to check that there
is not another protein molecule hiding somewhere in the asymmetric unit. What I
usually do in these cases is to set a very large map radius (say 40-60 Å) and
look at the complete solvent region to see
Dear all,
I have an original sca file with anomalous signal and a heavy atoms sites
file in PDB format.
PDB FILE :
CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2
SCALE1 0.012857 0.007423 -0.00 -0.0
SCALE2 -0.00 0.014846 -0.000.0
Dear Wei,
There is a new SHELX homepage with extensive documentation and downloading
instructions at: http://shelx.uni-ac.gwdg.de/SHELX/
SHELXE requires reflection files name.hkl (native) and name_fa.hkl (data
for phasing) and
and the heavy atoms in SHELX format in name_fa.res. I recommend
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Dear Wei,
if you are not too familiar with shelx c/d/e, I suggest the following
procedure, provided shelx c/d/e are installed:
- - get hkl2map from http://webapps.embl-hamburg.de/hkl2map/
- - run hkl2map from a terminal and from the directory where
Sorry, a better command line for running SHELXE in this case would have
been:
shelxe name name_fa -a5 -s0.5 -q -h -z
this ensures that the heavy atoms are refined before calculating the
initial phases, this often gives
much better maps. If you are not sure whether the space group is P6122
or
Hi Guangyu,
I think it's not as straightforward as comparing d/p ratios, that is only
one of several factors that influences precision. Another important factor
would be the overall level of thermal motion disorder which will most
likely be significantly higher in the 3.6A 80% case; after all
superpose and gesamt in ccp4
On 14 Mar 2013, at 20:53, Chen Zhao wrote:
Dear all,
I am now struggling to align two 3D RNA structures. I know there are a bunch
of web servers, but they either just generated a pdb file with a single
aligned structure, or they left the ligand out.
Does
Ian,
Because it is same protein, the high thermal motion is likely caused by crystal
packing, and should be corrected by TLS refinement. The B left over should be
similar.
Anyway, this is just a hypothetical question. I tried to make other things same
and just compare resolution and d/p. But
Well, wouldn't NCS be a parallel situation? I have heard, for example, that
the maps of viruses are considerably better at a given resolution than
monomeric proteins. So I would guess that someone has looked at this topic
in the case of NCS. Maybe high solvent content would be equivalent to
Dear George,
Thank you very much for your help!
Wei
At 2013-03-15 18:09:09,George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote:
Dear Wei,
There is a new SHELX homepage with extensive documentation and downloading
instructions at: http://shelx.uni-ac.gwdg.de/SHELX/
SHELXE requires
*Postgraduate Studentship available in the Ciulli Laboratory*
*Chemical Structural Biology of Protein-Protein Interactions*
A fully-funded PhD studentship is available immediately in our new
laboratory within the College of Life Sciences at the University of Dundee (
Guangyu,
If I'm understanding your question correctly; you're asking if all other
things are equal (resolution, degree of disorder, etc), does improving
the data/parameter ratio result in an improved model?
The short answer is: (at least sometimes) yes.
Pete
Guangyu Zhu wrote:
Ian,
what happened to all the even l h reflections?
Phil
On 15 Mar 2013, at 15:09, gengxiang zhao gzh...@gmail.com wrote:
Dear CCP4s,
I am looking for more experienced concerns to determine which space group my
crystal is. At present, we take it as P42212 (#94).
HKL is below:
Hi Gengxiang,
Personally I find it impossible to reliably assign a space group from
integrated reflections because you just don't know if the apparent
systematic absence violations are due to a TDS streak or overlapping
neighbouring strong spots. In the old days (i.e. when we had precession
Well - you seem to have absences for virtually all the (0 0 4n+1 4n+3) and
(2n+1 0 0) reflections which is consistent with P42 212 but you can be
misled. Is there any pseudo translation with either X or Z 0.5 - that could
give you similar absences. As Ian says, be wary..
Eleanor
On 15 March 2013
Dear All
I am planning to buy a linux workstation for crystallography. It seems that
Dell does not offer workstations with linux right now. Any good experience to
recommend?
Thank you!
Jie Liu
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Dear Jie Liu,
most Linux distributions are not too difficult to install, and with a
decent internet connection you only need to download a few MB for a
bootable CD for network installation - do you have a reason why you do
not want this yourself?
Dell Precision workstations are sold with RHEL, Ubuntu, or no OS
(FreeDOS), but you can't see those options from the public websites.
You need to try to get a Dell Premier account, talk to the Dell Rep
for your university about that, here's a screen shot from our uni's
premier site :
I've been pretty happy with the machines from
System76https://www.system76.com/.
They come with the most recent version of Ubuntu pre-installed.
However, as Tim says - installing Linux on any machine you can buy is a
pretty simple process now.
Cheers, Jim
On Fri, Mar 15, 2013 at 9:42 AM, Tim
As a follow up to Ian's suggestion, the LABELIT software (sorry for a non-CCP4
suggestion) will create artificial precession images from your raw oscillation
images.
Documentation can be found here:
http://adder.lbl.gov/labelit/
And an article describing the functionality can be found here:
Some of those system76 desktops look overclocked. I've always wanted to
try one to speed up processing but have been warned away from it for
fear of errors and stability. Does anyone have any experience of
overclocked desktops for PX software?
Alan
On 15/03/2013 17:55, Jim Fairman wrote:
On the subject:
Are there any protein-protein complexes commercially available (for cheap)?
The only one I could think of was hemoglobin.
Morten
On 14 March 2013 01:56, Wei Feng ccp4...@hotmail.com wrote:
Dear Lucas,
Thank you for your help!
Wei
At 2013-03-13 23:05:54,Lucas
Michael, yes sorry I had (temporarily) forgotten about LABELIT. In the
pseudo-precession image in the article (Fig. 3a) one can clearly see the
TDS streaks along the axes which could easily fool you into misassigning
the space group if all you have are the integrated intensities. Very nice!
Dear All, would you be able to recommend a primary anti-His6 Ab for western
blotting? Thus far, the ones we've used are not very specific to the
N-terminal hexahistidines and we pick up lots of background. Also, there's
one (others?) from Sigma that is conjugated to HRP, but costs ~$650. Thanks!
Hi Elias,
Not sure if you've looked at this option, but Pierce sells a polyHis tag
detection kit that is not based on an antibody, but instead is a
nickel-activated derivative of HRP. Has worked quite well for us in the past.
Brian Mark
On 2013-03-15, at 12:36 PM, Elias Fernandez
We haven't found a great primary (or secondary) antibody, but we have used the
NTA Atto 488 dye (Sigma 39625) with some success at primary detection of
His-tagged proteins directly in our gels, without the need for a transfer step
to a membrane. We run BSA alongside our samples to determine the
*Dear all,*
*I have collected a good quality dataset of a protein with 64% of solvent
in P 2 21 21 space group at 1.7A resolution with good statistical
parameters (values for last shell: Rmerge=0.202; I/Isig.=4.4; Complet.=93%
Redun.=2.4, the overall values are better than last shell). The
Check for translational NCS
And you are way too conservative with resolution. Even those holding
onto the Rmerge-dictated past would probably acquiesce to lower I/sig
cutoff. If you are using aimless, follow its recommendations based on
CC1/2, it's good for you.
Cheers,
Ed.
On Fri,
Wow, Usually on the default settings of adxv, I can see spots at this I/sig!
I suspect your data goes higher than 1.77.
Include more of the high resolution data. You very likely don't have the
correct space group.
F
On Mar 15, 2013, at 11:39 AM, Andrey Nascimento
What happens if you solvent-flatten/flip/massage that map, but tell the
software the solvent content much lower than what you think it is now? Maybe
you'll find another copy of the molecule?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Hi Andrey,
I am taking a risky guess:
From your slide #2, it looks like a termini (unless this correspond to the
beginning or end of disordered a loop) of the protein chain(s) is (are)
extending toward(s) the solvent channel. Are the density features shown in
slides #3,4, and 5 extend from this
Or give it to arp/warp, either with the current model to improve or with phases
from the current model to build new model?
Phoebe A. Rice wrote:
What happens if you solvent-flatten/flip/massage that map, but tell the
software the solvent content much lower than
what you think it is now? Maybe
I second Phoebe's suggestion. Looks like another molecule to me. If you are
doing molecular replacement you may need to get creative about trimming. When
we had a case like that it wasn't until the third person worked on it that we
go a solution because he trimmed the model differently than the
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* Aimless: Task interface fixed in part of input customisation section
* Molrep: Improvements to scoring system and bug fixes
* Logview: Command-prompt routine for viewing individual log files with QtRView
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