Jerry,
In my experience with GE's HiTrap Chelating HP columns (which use the
tridentate IDA linkage, rather than the tetradentate NTA), capture is
usually quite good as long as the protein is well behaved and the tag
isn't occluded. It is definitely possible to capture proteins at the
level of 0.
Hello All,
We have run into a problem running Phase under both CCP4 and Phenix.
Specifically with the Matthews calculation, which then causes Phaser
to look for something different then what we want. The input space
group is R3:H after processing. The input molecular weight of the
mod
I had heard that there was a world-wide Tungsten shortage, but this is
ridiculous!
JPK
On Wed, Apr 25, 2012 at 1:29 PM, H. Raaijmakers wrote:
> That's nothing. Once someone wrote me because the tungsten atom of my
> "Tungsten containing formate dehydrogenase" had dissapeared.
> Lost in translati
That's nothing. Once someone wrote me because the tungsten atom of my
"Tungsten containing formate dehydrogenase" had dissapeared.
Lost in translation during some autoscripted conversion.
It was corrected soon enough.:)
Cheers,
Hans
Jan Dohnalek schreef:
> There have been other manipulations
El 25/04/12 17:54, Michael Murphy escribió:
> I am trying to install Coot on a laptop that runs Ubuntu. Following the
> instructions on the CCp4wiki
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu
>
>
> sudo apt-key adv --keyserver keyserver.ubuntu.com
>
On Wednesday, April 25, 2012 09:40:01 am James Holton wrote:
> If you want to make a big splash, then don't complain about
> being asked to leap from a great height.
This gets my vote as the best science-related quote of the year.
Ethan
--
Ethan A Merritt
Biomolecular Structure Cent
Hi Michael,
If I interpret the content of Morten Kjeldgaard ppa repository
correctly the latest coot available there is for Natty Narwhal (11.04).
Hence, installation in 11.10 or later will just not work.
Cheers, Andrzej
On 4/25/12 5:54 PM, Michael Murphy wrote:
I am trying to install Coot
An effective tactic that has not been mentioned yet is simply to attach
your coordinates and map to a blanket email and send it simultaneously
to all of your competitors. The key thing here is "all". Send it to
EVERYONE who might serve as a reviewer for your structure. This may
sound like
While I'm quite happy with all the responses this question has provoked there
is an additional point I would like to contribute. It is not enough to say that
you can interpret your map with a model based on what you expect. You have to
also show that you can't interpret your map with any other
I think that anything that irrevocably modifies the experimental data
should be avoided whenever possible. Since anisotropic scaling is a
relatively fast calculation and there are several ways of doing it, it
is better to apply it locally when it is needed, e.g. in phasing (where
it is applied
You can get the aimless documentation from
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html
pending its official release through CCP4
No it does not do anisotropic scaling as such. That needs some sort of model of
the "ideal" intensity, probably best calculated from a model
I'm not sure that a
wondering if aimless performs anisotropic scaling or "elliptical"
rejections lately.
I ask because:
[1] last I knew, scala did not
[2] I can't seem to google up the aimless manual as readily as scala
... also, what consesquence would mosflm anisotropic resolution limits
have on scaling (if aimle
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Michael,
the command 'aptitude search coot' could give you an answer, although
I am not sure 'aptitude' is available on Ubuntu (it is in Debian).
Tim
On 04/25/12 17:54, Michael Murphy wrote:
> I am trying to install Coot on a laptop that runs U
I am trying to install Coot on a laptop that runs Ubuntu. Following the
instructions on the CCp4wiki
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 1DC81A57
sudo add-apt-repository ppa:mok0/ppa
a
Our policy is to request the pdb to update the stated resolution limit
after the deposition's gone through.
That said, I suspect it did not happen for many of our structures, because:
1) it's not part of the deposition mechanism, i.e. easy to forget.
2) the various programs (especially i
What freaked me out is that REMARK 2 seems to have changed over time: I have a
version of 1ihf.pdb (deposited around 1995) that was apparently downloaded in
1998, where remark 2 says 2.5, and a version downloaded yesterday where remark
2 says 2.2.
The whole thing actually started because the ne
My apologies, I guess there is a separate entry for resolution,
and in my depositions it gets filled from the remark 200 records
from CNS xtal_pdb_submission and I never thought to change it.
I guess now the PDB is enforcing the requirement that it
should be "the highest resolution used" and hence
I too believe that the value is set from the
high resolution limit form data collection or refinement.
All three numbers (high resolution limit in remark 2, remark 3
and Remark 200) are supposed to be consistent and are
defined as the highest resolution reflection used.
http://mmcif.rcsb.org/dicti
Curious that 83% solvent content would be out of range; A quick search in
the pdb indicates that there are 43 entries with solvent content >85% ...
Op 25 april 2012 09:41 schreef Jan Dohnalek het
volgende:
> There have been other manipulations with user-input values. We could not
> input solvent
We also use the US portal. Can't speak to the solvent content as we never
had a value much over 70%.
As for the resolution range, I never saw any place to enter this
user-defined resolution of the structure.
As far as i know it comes from the record:
REMARK 200 RESOLUTION RANGE HIGH (A) : 1
We indeed used the US portal for deposition which may be "the difference".
Nevertheless the recent reported resolution values etc. are projected also
to the PDBe portal.
Jan
On Wed, Apr 25, 2012 at 10:10 AM, Mark J van Raaij
wrote:
> Phoebe, Jan, PDB,
> is this something particular to the US po
*CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC*
Proposal Deadline **1st May 2012**
There will be beam time available at the ESRF for MX data collectionwith
a setup that allows online monitoring of UV/VIS absorbance
orfluorescence spectral changes of the crystal during the
X-ray
Phoebe, Jan, PDB,
is this something particular to the US portal of the PDB, or general?
We always use the European portal pdbe and have not had such "problems".
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madr
There have been other manipulations with user-input values. We could not
input solvent content 83% for 3cg8 (the real value!!!) as "being out of the
allowed range".
The resulting value in the PDB is "NULL" not showing the actually
interesting feature of the structure.
I also noticed that the repor
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