This is very uncommon...
Can you look at the final plot of R and Rfree against resolution.
Sometimes there is an awful hiccup somewhere -
ice rings?
high resolution data somewhat fictional -
low resolution data saturated and also somewhat fictional ..
I also check the completeness which is uin
Dear Arko,
Is it possible that your Phaser installation is out of sync with your CCP4
installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser
2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) ='
and 'SIGF(-) =' to the LABIN line.
Best regards
-- David
On
I just realised that my reply on this issue only went to Arko, and not to the
BB. I think that the problem was because of an internally out-of-synch CCP4
installation that was made available for Windows for some time. Here's my
reply, which makes a similar point to David's.
=
As Tim
Hi all!
Thanks a lot to Randy and Tim and David and to all who found it worthy
giving a thought! As Randy said it was due to an internally out of sink
CCP4 installation. The CCP4 6.1.2 is working fine
However I would like to bring into discussion another problem...While
trying to
Hi all!
Thanks a lot to Randy and Tim and David and to all who found it worthy
giving a thought! As Randy said it was due to an internally out of sink
CCP4 installation. The CCP4 6.1.2 is working fine
However I would like to bring into discussion another problem...While
trying to
Hi,
For reasons best known to George, SHELXD calls everything a sulphur. For some
phasing programs (no doubt including SHELXE) that doesn't matter, but it does
for Phaser. For this reason, the Phaser GUI allows you to substitute the
SHELXD atom with your own atom type. If you prefer
I input the alignment in ESPript. Add the template PDB file and it
makes a Bcol.pdb file where temperature factors are replaced my
sequence similarity. I open this file in Pymol in Surface and color
B-Factors as rainbow.
Ivan
On 12/7/11, Yuri Pompeu yuri.pom...@ufl.edu wrote:
I once saw a
Hi List,
I would like to build an artificial tetramer from a monomer PBD file.
All that I have is the coordinates it self with CRYST/CELL information
cards. The artificial 4-fold axis has an arbitrary orientation into the
cell. I mean, its not parallel to any crystallographic axis and have to
Hi Yuri,
I once saw a figure showing the protein as surface, but instead of having it
coloured by atom type
or potential, it was shown by percent conservation in the family. Something
like red highly conserved, all the way to white, not conserved at all...
Now, I assume the figure was done
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Hash: SHA1
Hello Fred,
if you know the rotation matrix, you can use pdbset with its 'rotate'
keyword.
It is not clear to me whether or not you have the rotation matrix or how
you define rotation.
Cheers,
Tim
On 12/12/2011 08:49 PM, Fred wrote:
Hi List,
I
Hi Tim,
Thanks for your message and sorry if I wasn't clear. I don't have
neither the axis orientation nor the rotation matrix. I would like to
create them but don't know how and which program to use. Theoretically a
have to create a axis (vector) at some distance of the molecule into the
at few Angstrons of the protein.
Em 12-12-2011 19:01, Jacob Keller escreveu:
How do you know where to put the axis?
JPK
On Mon, Dec 12, 2011 at 2:34 PM, Fredccp4bb.l...@gmail.com wrote:
Hi Tim,
Thanks for your message and sorry if I wasn't clear. I don't have neither
the axis orientation
This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry
operation (4-fold rotation) has 5 free parameters (translation along the
symmetry axis is irrelevant). The biggest problem is determining the values for
these parameters. For example, once you apply the symmetry,
All-
We are reevaluating the frequency of our pipette calibrations and were
tasked with determining the norm. How often do you calibrate your
pipettes? Do you have different schedules for different purposes (i.e.
crystallization pipettes get calibrated every 18 months, while purification
Hi James,
In my first post arbitrary orientation into the cell only means not
parallel to any crystallographic axis, which would simplify things very
much. I want to apply the 4-fold axis to the protein coordinates. If I
have a cell and therefore an origin, I can take a point at any distance
Can you clarify your reason for doing this?
JPK
On Mon, Dec 12, 2011 at 3:36 PM, Fred ccp4bb.l...@gmail.com wrote:
Hi James,
In my first post arbitrary orientation into the cell only means not
parallel to any crystallographic axis, which would simplify things very
much. I want to apply the
I only want to produce an artificial tetramer.
Em 12-12-2011 19:41, Jacob Keller escreveu:
Can you clarify your reason for doing this?
JPK
On Mon, Dec 12, 2011 at 3:36 PM, Fredccp4bb.l...@gmail.com wrote:
Hi James,
In my first post arbitrary orientation into the cell only means not
Hi List,
I want to preprare sel-met labeling protein. Could someone can tell me
if it is necessary to add DTT or BME to medium, which contains
sel-met, when growing cells?
Thanks in advance,
Yibin Lin
Generally no, only in the subsequent protein purification steps.
Tony.
Sent from my iPhone
On 12 Dec 2011, at 21:57, Yibin Lin yyb...@gmail.com wrote:
Hi List,
I want to preprare sel-met labeling protein. Could someone can tell me
if it is necessary to add DTT or BME to medium, which
Coot can do this using the Rubik's Cube principle: transform to some state
where the operation can be performed, perform the operation, then transform
back.
So, in coot, I would
(1) rotate the molecule to the appropriate orientation
(2) move to the appropriate place in the unit cell
(3) change
I suppose you mean the pipetman and similar, and having it calibrated
by a professional rather than pipetting into a weighing boat to see
if it is OK-
Unless i'm missing something, there is very little that can be done in
the way of calibration- the diameter of the stainless steel shaft and
the
The Phenix developers are pleased to announce that version 1.7.3 of Phenix is
now available. Binary installers for Linux, and Mac OSX platforms are available
at the download site:
http://phenix-online.org/download/
Some of the new features in this version are:
Graphical interface:
Hi Ed,
I just had a chance of looking at your comment more closely.
You are right it only uses PHIC if in refmacs set up you choose to refine with
prior phase information -AFAIU.
So what exactly is the info contained in the output refmacX.mtz besides map
coefficients for COOT? If it is not just
Hi All
I have a 3.0A dataset of a protein-protein complex. I used one of the
protein structure solved previously as a template and used phaser in CCP4
as well as in phenix. I used the sca file in phenix which gave a solution
with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i
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