Hmmm..does that mean that the journals are now the ultimate authority of
what stays in the PDB?
I find this slightly irritating and worthy of change.
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat
Echols
Sent: Dienstag, 5. November 2013 15:09
To:
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released. This is the first
update for both CCP4 and ARP/wARP in tandem.
The ARP/wARP component of this update will be available to those Mac and Linux
users who have previously installed both packages via the CCP4 Package
Hi,
I just installed the update using ccp4um.
All I get now is:
ccp4i
Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
does not have correct file label configure
Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
does not have correct file label preferences
Error
Hi Joachim
Thanks for reporting the problem
Please run
sudo /software/ccp4-6.4.0/bin/ccp4um
and uninstall the last update for now.
There should be something wrong with your config files.
I'll trace what it could be and then contact you.
Regards
Andrey
On 6 Nov 2013, at 13:13, Joachim
Dear all
If you had a problem similar to that Joachim and Ingo had (see below), please
run
sudo path/ccp4-6.4.0/bin/ccp4um
where path is the full path to your ccp4-6.4.0 installation,
and uninstall the last update.
Then you can launch ccp4i and install it again as usual.
Thanks!
Andrey
On 6
Dear all
A comment to my last e-mail
If your ccp4 installation is not write-protected,
do not use sudo, just run
ccp4um
Regards
Andrey
On 6 Nov 2013, at 14:49, Lebedev, Andrey (STFC,RAL,SC) wrote:
Dear all
If you had a problem similar to that Joachim and Ingo had (see below), please
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Dear Andrey,
since you mention the manual: is there a way to retrieve the manual
pages for the ccp4 programs? I often use 'man pointless' et al. to
check syntax etc and I miss the man pages in 6.4.0. Even the source
does not seem to contain them any
Hi there:
Has anyone got experience using the Formulatrix NT8 as a 'crystallization
robot'? Other options being considered are Art Robbins Phoenix TTP
Labtech's Mosquito, both of which I have used in the past.
Any feedback on NT8 will be highly appreciated.
Thanks and Regards,
Dileep
Dear ccp4 users
a question about the recovering of true intensities from merohedral
twinned crystal. Providing alpha and the twin operator one should be able to
recover the
intensities from the formulas:
I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp hofkristall...@gmail.comwrote:
Hmmm….does that mean that the journals are now the ultimate authority of
what stays in the PDB?
I find this slightly irritating and worthy of change.
http://www.wwpdb.org/UAB.html
It is the current wwPDB
Dear Fulvio,
you cannot detwin perfectly twinned data with this formula. The term (1-2α)
becomes zero, so you are dividing by zero. With good refinement programs
(ShelX, Refmac), refinement is done against twinned data, which is better than
to detwin the data with the formula you mention.
As I
I've remained silent as this thread evolved into a discussion of how the PDB deals with
water names and numbers. But Nat's comment about the PDB not advertising itself as
anything other than an archival service finally prodded me into saying something.
Something I've slowly come to realize is
Thank you for reply. My question mostly concern a theoretical aspect rather
than practical one. To be not misunderstood, what is the mathematical model
that one should apply to be able to deal with twinned intensities with their
errors? I mean, I+_what? I ask this In order to state some general
Dear CCP4 / Coot community,
I am trying to use LIDIA from Coot 0.7.2 - as supplied with CCP4-6.4.0 - to
look at a protein / ligand complex.
However, when trying to launch LIDIA from the Extensions menu of Coot - I get
the following error.
I guess this suggests some form of fortran compile
Hi Dileep,
We have been a user of the NT8 robot going on a year now, and we're quite
happy with it. The initial versions of the machine had a few problems, but
engineers over at Formulatrix have worked out a majority of the bugs and
the current version of the machine functions quite well. We
Hi,
I have a structure which should have space group P212121, but it has been
processed to P21212. It can not be solved and refined. Right now I do not
have HKL2000, but I need change the space group to P212121. Is there a way
for me to do this using CCP4?
Thank you,
Maggie
Hi Maggie
echo symm P212121 | mtzutils HKLIN in.mtz HKLOUT out.mtz
should do the trick.
Cheers
-- Ian
On 6 November 2013 18:13, MAGGIE dongmeij...@gmail.com wrote:
Hi,
I have a structure which should have space group P212121, but it has been
processed to P21212. It can not be
Hi Maggie,
you can re-process your data using XDS and can provide the desired space group
in the XDS.INP file. It won't take much time.
Vikrant
Vikrant Upadhyay
Postdoctoral associate
Dr. Crina Nimigean's lab, A-1050
Department of Anesthesiology
Weill Cornell Medical College
525 East 68th
If you're only changing the 2-fold axis along c to a 2-fold screw axis, you
don't need to go back to the raw image files and reprocess them! Just tweak
the header of the .sca file and carry on (and take notes on what you did).
From: CCP4 bulletin board
I liked Ian Tickle's 1-line ccp4 script for changing the space group with
mtzutils.
I believe CAD can do this also. In any case, there's no need to reprocess.
Some reflections present in the current data will be systematically absent in
the new space group, but presumably they will be eliminated
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Dear Fulvio,
with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
would it not?
Although especially for theoretical aspects you should be concerned
about division by zero.
Best,
Tim
On
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Dear Maggie,
in addition to what others explained, data integration does not depend
on the space group. It only depends on the Laue group, and P21212 and
P212121 belong to the same Laue group. You would see no difference at
all in reprocessing, and
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Dear Almudena,
depending on your application there might be a different approach from
what I suggested before:
you could use my 'spots4cellnow'
(http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/spots4cellnow/) to
convert the SPOTS.XDS into
Dear all,
there is a tool to identify invariant
water molecules in homologous protein structures
and the tool can be accessed via
http://cluster.physics.iisc.ernet.in/3dss/
best,
Sekar
Thanks Bernhard
you have helpfully distinguished between the two processes - there is
certainly a
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
Tassos,
I'm no expert either, and there are caveats for using this formula on
correlated magnitudes. But I would assume that the intensities of twin
related reflections should be independent from each other (that's my
understanding of the sigmoid cumulative intensity distribution of
twins).
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