Dear Appu,
It seems that the anisotropy server you used put the anisotropic corrections in
the pdb, which got subsequently rejected by the refinement programs because of
insufficient resolution.
The alternative is to apply anisotropic scaling to your reflection data, which
is e.g. done by the
Dear all;
I have reinstalled ccp4i recently and everything seems to work fine but
ViewHKL. Every time I try to visualize a .mtz file the program gets
opened but without loading the .mtz. Then it gets frozen and I have to
kill it. In the command line the messages I get are:
**SYMMETRY
For the benefit of the whole bullitin board…
Von: Schreuder, Herman RD/DE
Gesendet: Donnerstag, 2. Juli 2015 09:26
An: 'Isaac Westwood'
Betreff: AW: [ccp4bb] Real space refinement of alternative conformations
Dear Isaac,
I have done some tests and you are right, the peptide get seriously
You are right. After I sent the email to the bulletin board, I realized that in
R32 there must be more then unit cells but did not send a correction.
Next time, I will check the space group before sending an email.
Best regards,
Herman
Von: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
Hi everyone,
I am running Phaser (from Phenix) and while checking the .log file (it is
still running) I realize that it found some solutions with a TFZ score over
7, but it won't take them I guess because the number of clashes is higher
than allowed (12, I guess they're not so many either).
My
Hi Herman and Boaz,
in the trigonal setting R32 (not in the hexagonal setting H32), the
unit cell in R32 contains 6 copies. If you take the whole R32 unit cell
as a P1 cell, you would have 6 copies in the asymmetric unit, as
Hermann wrote.
Best regards,
Dirk.
Am 02.07.15 um 15:52 schrieb
Dear All,
I would like to inform you that a postdoctoral position is available at
the EMBL Hamburg Unit in the research group of Dmitri Svergun.
I attach a description of the Vacancy Notice below. Deadline for
application is August 15th.
--
*Job description***
The European
Dear Almu,
In the development version of Phaser currently available in nightly builds of
Phenix (and soon in an upcoming stable release of Phenix, as well as in CCP4),
solutions that fail to pack, even though they have such high TFZ scores that
they should normally have been convincing, are
Dear Marta,
as a workaround, before starting ViewHKL change locale settings
to have '.' as a decimal point.
For example, from command line:
LC_ALL=C viewhkl
or
LC_NUMERIC=C viewhkl
It's a bug in ViewHKL and/or in symop_to_mat4() in libccp4.
Marcin
On Thu, Jul 02, 2015 at 11:43:08AM +0200,
Dear Almu,
Apparently, you have more than one search model. What worked very well for me
was to superimpose these models and cut out the loops which are variable
between the models. These loops may be different again in your protein and may
be behind the clashes in Phaser. Without these
Hi Herman,
While you're correct regarding increase in number of entities in the asu upon
lowering the symmetry, you're not correct for specific case of R32. One
molecule per asu in R32 equals 18 molecules per asu in P1.
Regards,
Vaheh Oganesyan
www.medimmune.com
From: CCP4 bulletin board
Dirk, you're right. With rhombohedral setting there are only six copies of
asymmetric units in the unit cell. So, technically, Herman was not wrong.
Regards,
Vaheh Oganesyan
www.medimmune.com
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk
Kostrewa
Sent: Thursday,
On Thu, 2 Jul 2015 00:15:58 +0100, Eric Karg harvard...@yahoo.com wrote:
Hi all,
I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do
paired refinement to determine the optimal resolution cutoff. Here is what I
get at different resolutions set in Phenix:
Final
1) Commercially made oligonucleotides
2) M13 rolling circle replication (how people used to make ssDNA for sanger
sequencing).
———
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Hi,
Sorry for the non-crystallography question, does anyone know how to produce
milligram quantities of single stranded DNA? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 12318
New York, NY 10031
I think your idea was discussed herein before, but that the consensus was that
CC1/2 does not change much when you scramble and re-calculate.
What one needs is a good way to determine at what point in the CC1/2 curve the
data stops being useful in obtaining the best possible model, and it seems
Hi all,
I have read recent SERCA paper on IUCrJ and found their discussion
interesting.
Structural studies of P-type ATPase–ligand complexes using an X-ray
free-electron laser by Maike Bublitz et al.
http://journals.iucr.org/m/issues/2015/04/00/jt5009/index.html
In addition to CC1/2 and paired
Thanks for everybody's suggestions! I finally fixed coot following Zhijie's
suggestion, where I set one window mode in Xlaunch. For pymol, I just
gave up... I am not sure whether the NVIDIA graphic card is making things
more complicated...
Best,
Chen
On Thu, Jul 2, 2015 at 1:29 AM, Zhijie Li
Another criterion for cutoff, also requiring the structure to be solved,
is the agreement between data and structure, e.g. Rfree or CCfree.
I think it is very unlikely that you could get Rfree =.2493 in a shell
which contains only noise. So I would suggest doing paired refinement
to 2.2 and 2.1 A
On 02/07/15 18:01, Pankaj Chauhan wrote:
I have installed ccp4 and phenix on ubuntu 14.04 LTS.
When I open coot while using phenix or ccp4 and try to load a molecule
from a Search Monomer library, it is unable to load the molecule and
this pop up You need to setup CCP4 (Specifically
Well, in that case, one could simply look at the plot of CC1/2 versus
resolution and see the step up to one, conclude something was off.
I wonder whether PDB REDO was able to get some empirically-determined values
for CC1/2 cutoffs by comparing paired refinement versus CC1/2 versus other
While I was puzzling over an entry in the PDB some years ago (since
obsoleted) I noticed that all the high resolution amplitudes were equal
to 11.0! This was before CC1/2 but for this structure it would have
been equal to one, and yet the outer data were useless. A practical
test like paired
Hi,
I have installed ccp4 and phenix on ubuntu 14.04 LTS.
When I open coot while using phenix or ccp4 and try to load a molecule from
a Search Monomer library, it is unable to load the molecule and this pop up
You need to setup CCP4 (Specifically LIBCHECK) first.
I will appreciate if someone
My take on this-
No one has been willing to specify a cutoff (and probably there is no rigorous
way to
mathematically define the cutoff) and say If CC* (or CCfree or whatever) is
below X
then it will not improve your structure, if above X then it will. Probably
depends
among other things on
But it is not the R-free of the shell here. In paired refinement you take the
R-free of the reflections outside the shell.
Cheers,
Robbie
Sent with my Windows Phone
Van: Edward A. Berrymailto:ber...@upstate.edu
Verzonden: 2-7-2015 18:43
Aan:
Yes, my stupid mistake. Please delete/disregard!
On 07/02/2015 12:46 PM, Robbie Joosten wrote:
But it is not the R-free of the shell here. In paired refinement you take the
R-free of the reflections outside the shell.
Cheers,
Robbie
Sent with my Windows Phone
Wasn’t all of this put to bed through the implementation of CC measures?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie
Joosten
Sent: Thursday, July 02, 2015 12:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] paired refinement
But it is not the R-free of
Dear Paul,
The software is coot-Linux-x86_64-ubuntu-14.04.
Have I made any mistake in installing or executing any file of coot during
installation (there is a file, LIBEXEC).
thanks
Pankaj
On Thu, Jul 2, 2015 at 1:41 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk
wrote:
On 02/07/15 18:01, Pankaj
Dear Giulliana Rangel,
if your protein is made recombinantly you could try a SeMet prep. The
fixed atoms solve many issues you could have with soaking.
Best,
Tim
On 06/29/2015 02:47 PM, Giulliana Rangel wrote:
Dear all,
I'm looking for a method to solve the phase problem. Thus, I would like
Hi Jacob,
An automated test for finding a resolution cut-off: Paired refinement. I may be
somewhat biased here, but I think it is fairly conveniently implement in
PDB_REDO ;)
Cheers,
Robbie
Sent with my Windows Phone
Van: Keller,
Dear Giulliana,
I imagine this may well be of assistance:-
*J. Appl. Cryst.* (2009). *42*, 540-544[ doi:10.1107/S0021889809012370
http://dx.doi.org/10.1107/S0021889809012370 ]
HATODAS II - heavy-atom database system with potentiality scoringM. Sugahara
Dear Smith,
when you expand to P1, pointless should suggest the space group you
expanded from, unless you fiddled with the data after expansion.
Regards,
Tim
On 07/01/2015 04:43 AM, Smith Liu wrote:
If both the PDB and mtz for the pdb have been assigned to P1 space group for
some reason, can
Hi Robbie,
I have been wondering how much information would be present in a
weighted CC1/2 with weights from the ML refinement program.
As I understand the concept behind paired refinement, one can use much
higher resolution data in refinement than you would expect from the
(classical) scaling
Hello again.
How does one prepare restraints for a Ni ion with four ligands:
- NE2 atoms from two His residues
- N and O from one Gly residue
REFMAC nailed down the distance. How do I specify a near square-planar
arrangement of the ligands?
Thank you,
Wolfram Tempel
34 matches
Mail list logo
