Dear colleagues,
We are looking for a GPCR structural biologist to come and join our team in
Molecular Pharmacology. Please see job description that follows. Please
don't send me your CV, but rather apply on-line via the provided link. Thank
you! -Dirk
https://lill
resolution (that I plot then with gnuplot). I can't recall having used
coordconv at all.
Best regards,
Dirk.
On 8/26/21 12:29 PM, Robbie Joosten wrote:
Dear CCP4 users,
We (as in, the CCP4 developers) are investigating some (potentially) missing
functionality in CCP4i2 and/or Cloud
given), where for each test set reflection,
after applying the NCS rotations in reciprocal space, the distances to
the working set reflections are taken into account, and test and working
set reflections are chosen such that their distances are large enough to
be uncorrelated.
Best regards,
Dirk
lease don't hesitate to contact me.
-Dirk
Dirksen Bussiere, Ph.D., M.B.A.
Sr. Director/Head, Molecular Pharmacology (Quantitative and Structural Biology)
Lilly Research Laboratories
Eli Lilly and Company
Lilly Biotechnology Center Phone: 510-759-7013
10290 Campu
7C1000&sdata=1IHr8eXSkWCrH2S8UTDeADrnWRgg7sqVGTkyaHk%2FZic%3D&reserved=0>
If you have any questions, please don't hesitate to contact me.
-Dirk
Dirksen Bussiere, Ph.D., M.B.A.
Sr. Director/Head, Molecular Pharmacology (Quantitative and Structural Biology)
Lilly Research Laboratories
a conversion program or route. Thank
you.
-Dirk
Dirksen Bussiere, Ph.D., M.B.A.
Sr. Director/Head, Molecular Pharmacology
Lilly Research Laboratories
Eli Lilly and Company
Lilly Biotechnology Center
10290 Campus Point Dr. E-mail:
bussiere_dirk...@lilly.com
atoms. I
never tried this with REFMAC5, though.
Cheers,
Dirk.
On 07.04.21 11:46, Eleanor Dodson wrote:
Well - I use COOT for this sort of task, and dont trust the automated
tools.
my procedure is
load COOT - probably after a refinement cycle
set occupancy of ligand(s) to 0.00 ( Measures
doubt.
Cheers,
Dirk.
On 03.12.20 10:20, Robert Nicholls wrote:
Hi Dale,
You're absolutely right - the multiple hypothesis testing problem is
one that is often not considered, let alone properly accounted for.
Whilst this can be accounted for by appropriate adjustment of
significance lev
r the OSCILLATION_RANGE, data
processing might run through but produces non-sense results, independent
of the data processing program you use. So, it is absolutely important
to know the correct value for the oscillation range per frame.
Cheers,
Hi Paul,
thanks - I've setup my own key bindings, already ;-)
Cheers,
Dirk.
On 11.09.20 12:34, Paul Emsley wrote:
Maybe because I've never attended a Coot course? And maybe because,
I've even never searched for Coot tutorials because the usage of Coot
was (almost) always ve
,
I will have a look at the pointers that you gave below. I would also be
grateful if you could give some pointers (which I've probably
overlooked!) where Eigen-flip, JED-flip, backrub and CURLEW are explained.
Best regards,
Dirk.
On 10.09.20 17:59, Paul Emsley wrote:
I'm not again
Dear Marian,
for some while, now, in xorg.conf, the entry
Option "Composite" "Disable"
does not work. Please, use instead the entry
Option "COMPOSITE" "Disable"
Cheers,
Dirk.
On 03.08.20 14:54, Marian Oliva wrote:
INSTALING STEREO COOT 3D VISION 2
rules.d/98-nvstusb.rules, with the contents
# NVIDIA 3D Vision USB IR Emitter
SUBSYSTEM=="usb", ATTR{idVendor}=="0955", ATTR{idProduct}=="0007",
MODE="0666"
Cheers,
Dirk.
On 30.07.20 14:46, Marian Oliva wrote:
Dear colleagues.
I would like to
If I remember
correctly, this is something that Gerard proposed long time ago for
phasing programs.
Best wishes,
Dirk.
On 01.07.20 11:52, Kay Diederichs wrote:
Dear Dirk,
one cannot fully correct radiation damage. Normal scaling procedures take care of the
average decay by a smooth resolu
, to average them and count them only once (say, for crystals
measured multiple rounds of 360 degrees to find identical geometries)?
Best wishes,
Dirk.
On 01.07.20 11:02, Gerard Bricogne wrote:
Dear Dirk,
Aren't you for getting about radiation damage? The n measurements of
the sam
realistic
number of truly independent measurements.
Cheers,
Dirk.
(*) I don't see a difference between measuring the same reflection with
the same geometry n-times and measuring it n-times as long (apart from,
maybe, catching instabilities in the experimental setup). Just averaging
Hi,
I noticed that, while saving my pdb model in COOT 0.9, sometimes a big
part of the header (compared to the originally loaded file) is just left
out in the new pdb-file. This results in that COOT cannot reopen this
file at another time. Any ideas how I can fix this?
Best regards
Dirk
Dear Maria,
are you sure, it's I222? From the extinction rules, you can't
distinguish between I222 and I2(1)2(1)2(1).
Best regards,
Dirk.
On 22.05.20 12:08, Demou, Maria wrote:
Dear all,
I have a question that may have a straight forward answer, and was
wondering if this is a co
anager
XFCE: Settings -> Window Manager Tweaks -> Compositor -> Enable display
compositing
I hope that helps.
Cheers,
Dirk.
On 1/15/20 8:52 AM, "Weiergräber, Oliver H." wrote:
Note that the more recent versions of EL7 no longer require compositing to be
disabled for nVidia s
<https://nvidia.custhelp.com/app/answers/detail/a_id/4845/~/3d-vision-end-of-life---faq>
on the Nvidia site.
Best regards,
Dirk Kostrewa.
On 1/9/20 10:37 AM, Barone, Matthias wrote:
Hi Patricia
All modern graphics cards still support 3D vision, but you are correct
that nvidia is addr
dify the composite option in your
xorg.conf as follows:
Section "Extensions"
Option "COMPOSITE" "Disable"
EndSection
I have no idea, since when Xorg is case-sensitive, or whether this has
anything to do with the Nvidia driver (I use the one from ELRepo).
Sorry for spamming the CCP4BB with this e-mail meant for Kay, only - I
accidentally used the "Reply All" button instead of the "Reply" button
... ;-)
Anyway, I wish the CCP4 community a Happy New Year!
Cheers,
Dirk.
Forwarded Message
Subject: Re: [c
Stereo-Brille nicht funktioniert ...
Mit unseren alten 3D-Ready-Monitoren haben wir unter Scientific Linux
7.6 bisher keine 3D Stereo-Probleme beobachten können. Die
Nvidia-Treiber kommen aus dem ELRepo-Repository. Habt Ihr die
Stereo-Probleme noch?
Liebe Grüße,
Dirk.
On 20.12.18 22:28,
The Structural Research Group at our Oncology Site Vienna is seeking an
experienced Protein Crystallographer in the field of pharmaceutical research
and drug design. We are looking for a candidate with outstanding professional
and personal competencies, highly motivated and with the ability to a
Dear CCP4ers,
many thanks to all of you who replied to my request!
I wish you a Merry Christmas and a Happy New Year!
Dirk.
Forwarded Message
Subject:[ccp4bb] Calculation of generalised R-factor?
Date: Tue, 20 Dec 2016 14:47:00 +0100
From: Dirk Kostrewa
Reply
purpose ...
Cheers,
Dirk.
On 20.12.2016 15:37, Robbie Joosten wrote:
The value for the Hamilton test is written by Refmac as the weighted
R-factor. There was a follow-up paper that showed that you shouldn’t
use the normal R-factor for the Hamilton test.
PDB_REDO does the Hamilton test
reported by the
usual refinement programs.
Is there a program that reads an mtz file with Fo and refined Fc and
just calculates RG?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Lud
and quality of results without the help
of Global Phasing.
Best wishes,
Dirk
---
Dr. Dirk Reinert
Boehringer Ingelheim Pharma GmbH & Co. KG
Lead Identification and Opt. Support
Tel.: +49 (7351) 54-97892
Fax: +49 (7351) 83-97892
mailto:dirk.rein...@boehringer-ingelheim.com
Boehringer Ingel
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.
"Disable"'.
However, disabling composite is incompatible with gnome 3! So to get 3D
stereo working, I completely removed gnome 3 and switched to KDE 4. If
you don't like KDE, I got 3D stereo also working with the MATE desktop
on one trial system.
Best regards,
Dirk.
On 02.
Dear Bernhard,
further thinking about the Babinet scaling effects, I have to correct my
conclusion in the last sentence:
On 12.01.2015 14:21, Dirk Kostrewa wrote:
If, however, the unmodelled part is less well ordered (which is the
more common case), it's contribution will mainly affec
). This, in principle, should increase, or overestimate, the
signal of the difference densities at low resolution, which might also
help with interpretation of the unmodelled part.
But all these scaling effects should be small, unless a substantial part
of the model is missing.
Best regards,
Dirk
in of possibly important difference density peaks in narrow regions.
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
worse for simulated-annealing).
I also think, that neither simulated-annealing nor jiggling is necessary
to get rid of previous bias.
Best regards,
Dirk.
On 25.11.2014 17:03, Ian Tickle wrote:
Dear All
I'd like to raise the question again of whether any of this 'jiggling'
(i.e. ad
rather low personal estimate of the accuracy (not precision) of unit
cell parameters.
Best regards,
Dirk.
Am 23.07.2014 09:49, schrieb Bernhard Rupp:
Although Zby's remarks re precision are beyond my original bewilderment
about listed zepto-meter range digits (sans precision measur
a few
weeks ago, but got no reply, yet (maybe, my e-mail got lost).
Cheers,
Dirk.
Am 03.07.2014 13:46, schrieb Tim Gruene:
Hi Dirk,
that would truely be very sad - the XDS file format is such a beautiful,
self-contained and well documented format for diffraction data that a
misinterpretation s
... and please check, whether phenix.xtriage recognized the input data
as intensities or as amplitudes.
In case of doubt, convert the intensives first into an mtz file with Fs
instead of Is and run phenix.xtriage on the mtz file.
Best regards,
Dirk.
Am 03.07.2014 13:36, schrieb Tim Gruene
op fiber diffraction, ice rings, etc.) or extremely weak data.
For a really good discussion of twin tests, see Yeates, Methods.
Enzymol. 276, 344-358, 1997.
Best regards,
Dirk.
Am 28.01.14 18:26, schrieb Bert Van-Den-Berg:
Dear all,
I recently collected several datasets for a protein that
an-readable extended PDB format would really help.
Cheers,
Dirk.
Am 30.08.13 18:14, schrieb MARTYN SYMMONS:
Hold your horsemen!
Does not this option save us from 'formatagedon'?
We currently only have single letters or numbers for chains. But we
could easily agree to switch to dou
Hi Martyn,
excellent - this worked!
Many thanks!
Cheers,
Dirk.
Am 30.08.13 16:04, schrieb Martyn Winn:
IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There may
be something specific in pdbset which interferes. You can try pdbcur as an
alternative. Something like
e chain names. To my
knowledge, only COOT and PHENIX can cope with them.
Before I start writing my own little jiffy, is there a quick way to use
COOT or PHENIX to apply a fractional coordinate shift, or could you tell
me, which other program I can use in this special case?
We have a very similar setup, and I can only second Kay's experience.
Best regards,
Dirk.
Am 31.07.13 13:36, schrieb Kay Diederichs:
I have a very different experience with NFS: we are using Gigabit Ethernet, and
a 64bit RHEL6 clone with ECC memory as a file server; it has RAID1 ext4
esolution increments in refinement to decide
the high resolution cutoff is very time-consuming.
Best regards,
Dirk.
Am 13.06.13 17:15, schrieb Andrea Edwards:
Hello group,
I have some rather (embarrassingly) basic questions to ask. Mainly.. when
deciding the resolution limit, which statistic
regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr
mechanism for Coot, be it part of CCP4 or part of
Coot, would help the software administrator :-).
A related question just crossed my mind: when will Coot and CCP4mg
become part of the CCP4 core packages?
Best regards,
Dirk.
P.S.: I've sent Paul Emsley a CC of this little conversation.
Dear CCP4 developers,
this question might be interesting for many CCP4/Coot users:
will the Coot release 0.7 and future releases be made available to CCP4
users via the CCP4 software update?
Best regards,
Dirk.
Original-Nachricht
Betreff:[COOT] Release 0.7
Datum
lly linked
(uses shared libs), for GNU/Linux 2.6.9, not stripped"
I hope that helps a little bit.
Best regards,
Dirk.
Am 20.09.12 14:37, schrieb David Waterman:
Dear Fred,
You may like to try the CCP4 Package Manager, available from the
downloads page: http://www.ccp4.ac.uk/download/#o
Dear Fulvio Saccoccia,
along the lines of Ian Tickle's reply: there should be a script
"cns_solve_env_sh" using /bin/sh, which is usually a soft-link to
/bin/bash. I use this script for setup of CNS under bash.
Best regards,
Dirk.
Am 12.07.12 16:49, schrieb fulvio saccoc
g and
shrinking the mask, could produce false positive or negative difference
density. To exclude these cases, you can always calculate the Babinet
bulk solvent correction as a control.
Best regards,
Dirk.
Am 16.04.12 12:37, schrieb Allister Crow:
Board members,
I have a couple of questions
, a kappa of 180 degrees would be expected. This
looks (very) improper to me.
Best regards,
Dirk.
Am 21.02.12 14:47, schrieb Francis E Reyes:
Hi all
This structure has the following ncs (output via phenix.simple_ncs_from_pdb)
OPERATOR 1
CENTER: 18.3443 -55.4605 23.0986
ROTA 1:1.
the expected cooling
rate a lot!
My very personal experience is, that cryo-cooling in the N2-stream
worked better for me than in LN2 in a variety of projects - but the
reason could just be me ;-)
Best regards,
Dirk.
[1] Matthew Warkentin, Viatcheslav Berejnov, Naji S Husseini, and Robert
E
dered and disordered parts, respectively, without any need to
change the wavelength. In this analogy, the ordered part would have the
coherence of a Laser, whereas the disordered part would have the
incoherence of a vapour lamp.
Best regards,
Dirk.
Am 12.01.12 11:57, schrieb Ian Tickle:
On 1
My understanding of coherence is a constant phase relation between
waves. Of course, this breaks down for inelastic scattering, but
(in)coherence can also be described without any change in wavelength.
Best regards,
Dirk.
Am 12.01.12 11:27, schrieb Bernhard Rupp (Hofkristallrat a.D.):
Does
uthors were annoyed by a vanishing NMR signal because the
macromolecule crystallized in the NMR test tube ;-)
Best regards,
Dirk.
Cheers, BR
PS: I am grappling with the meaning of resolution in NMR. I can see that it
could be related to comparable data/parameter ratios, although I am even
cture factors? For a larger unit cell (assuming a similar
solvent content), I would then expect larger structure factors.
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität Mü
he restraint definitions are often incomplete.
Greetings
Dirk
Am 22.11.11 01:16, schrieb Jan van Agthoven:
Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Jan
.,
D58, 872-874 (2002); Glusker, Advances in Protein Chemistry, 42, 1-76
(1991)).
But depending on your data resolution and quality, and on the
completeness of the coordination sphere, it might be difficult to
distinguish between them.
Best regards,
Dirk.
Am 16.11.11 19:20, schrieb Jacob Keller
t eigenvalue), and the minor inertia axis coincides with the
Z-axis (smallest eigenvalue)."
Best regards,
Dirk.
Am 27.10.11 14:17, schrieb Anasuya Dighe:
how do i put a protein molecule inside a cube with x-axis spanning till the
largest x-coordinate, y-axis spanning till the largest y
Yes, SHARP and BUSTER both work on a Mac.
Cheers,
Dirk.
Am 29.09.11 09:45, schrieb Sebastiano Pasqualato:
On Sep 29, 2011, at 2:48 AM, Nat Echols wrote:
I don't know of any macromolecular crystallography programs that
don't run on Mac -
Hey there,
does this mean that SHARP work
secondary
structures and other hydrophilic interactions to some reasonable
geometry, even at very low resolution.
Best regards,
Dirk.
Am 26.09.11 16:17, schrieb Nat Echols:
On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa
mailto:kostr...@genzentrum.lmu.de>> wrote:
when I pl
all geometrical restraints, of course.
Best regards,
Dirk.
Am 22.09.11 22:49, schrieb Nat Echols:
On Thu, Sep 22, 2011 at 4:18 PM, Pete Meyer <mailto:pame...@mcw.edu>> wrote:
In short, the effective observation to parameter ratio improves by
~4%. This seems like a relatively small
Great! Maybe, they should add an extra term for correlation of Fcalc to
Fobs (or LLG or R) to their game. I wonder, if structures could be
solved ab inition by players, then :-).
Best regards,
Dirk.
Am 19.09.11 12:33, schrieb Kevin Cowtan:
"Crystal structure of a monomeric retro
case a "X". Maybe,
you could check your sequence for this ...
Best regards,
Dirk.
Am 12.08.11 11:16, schrieb Phil Evans:
I was missing the semicolon, but it still fails
On 12 Aug 2011, at 10:12, Antony Oliver wrote:
Interesting iPhone formatting things going on... Let's tr
Dear all,
or use a modified version of Clemens's commands for that:
find . -perm 700 -exec chmod 755 {} \;
find . -perm 750 -exec chmod 755 {} \;
find . -perm 600 -exec chmod 644 {} \;
find . -perm 640 -exec chmod 644 {} \;
Best regards,
Dirk.
Am 19.07.11 14:34, schrieb Clemens Von
Dear colleagues of the CCP4BB,
many thanks for all your replies - I really got lost in the trees (or
wood?) and you helped me out with all your kind responses!
I should really leave for the weekend ...
Have a nice weekend, too!
Best regards,
Dirk.
Am 15.04.11 13:20, schrieb Dirk Kostrewa
cular
transform to the sampling of the electron density within the unit cell.
For the 1-dimensional case, this is discretely sampled at a/h for
resolution d, which is still 1x sampling and not 2x sampling, as
required according to Nyquist-Shannon. Where is my error in reasoning,
here?
Best regards,
(2h).
So what is the argument again, that the sampling of the continuous
molecular transform imposed by the crystal lattice is sufficient to get
the desired information at a given resolution?
I would be very grateful for your help!
B
Hi Ethan,
many thanks for that - your Dark Matter really (en)lightened my day! I
wonder, how many pdb records in the future will contain the
corresponding remark lines that your incredible perl script produces :-)
Best regards,
Dirk.
Am 01.04.11 08:06, schrieb Ethan Merritt:
Hi to all on
cdotal evidence, or there is still room for improvement
in existing ML refinement programs.
Best regards,
Dirk.
Am 28.02.11 11:40, schrieb Randy Read:
Hi,
I'm on Garib's side here. The way the maximum likelihood targets work, the
variances are defined relative to the average intens
cture factors, the refinement
statistics can only be reproduced using these structure factors). The
original structure factors can be easily reproduced by applying back the
negative sharpening B-factor.
Best regards,
Dirk.
Am 26.02.11 01:09, schrieb Garib N Murshudov:
I would not sharpen stru
ith
Ni than with Cl.
However, if the data set was collected on a home source with CuKalpha
wavelength, such a map would be not be very helpful here, because the Ni
signal is about as weak as the Cl signal.
Best regards,
Dirk.
Am 24.02.11 16:37, schrieb Gloria Borgstahl:
I'm voting with R
Dear CCP4ers,
on behalf of Patrick Cramer, I send a Postdoc position offer, given
below. Please, do not respond to me, but to the e-mail addresses given
in the job description.
Best regards,
Dirk Kostrewa.
***
Applications are invited
Thanks a lot for your suggestions! Meanwhile, my colleague entered the
desired sequence information into the first website without frames, and
after that, the usual frame layout re-appeared! I don't know whether
this is a bug or intended ...
Best regards,
Dirk.
Am 15.02.11 17:00, sc
different deposition fields, which makes deposition a nightmare. Has
anybody else noticed that?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen
the
right one?
I would be grateful, if you, Ian, or any other crystallographer on this
board could help me (and maybe others) to solve this riddle.
Best regards,
Dirk.
[1] Tickle, Laskowski, Moss. "Rfree and the rfree ratio. I. Derivation
of expected values of cross-validation re
,
Dirk.
Am 28.01.11 14:37, schrieb Van Den Berg, Bert:
I have heard this before. I'm wondering though, does anybody know of a
systematic study where different data processing programs are compared
with real-life, non-lysozyme data?
Bert
On 1/28/11 7:58 AM, "Bosch, Juergen" wrot
XLEV exceeded
Does anyone could point me to a direction what that means?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Mu
liced probably won't help.
Anyway, good luck!
Dirk.
Am 05.11.10 09:40, schrieb Sergei Strelkov:
Dear All,
I am processing a dataset collected (not by me) with 0.1 degree
oscillations.
The diffraction is quite weak even though there is a clean diffraction
pattern to about 3A.
Either Mo
data are severely incomplete, I must admit,
that I don't worry too much.
The twinning problem is really severe! Here, I don't see how this could
be done in a clever way in real space.
Interesting discussion ...
Best wishes,
Dirk.
Am 29.10.10 10:41, schrieb George M. Sheldrick:
real space refinement ...
Best regards,
Dirk.
Am 29.10.10 08:03, schrieb Robbie Joosten:
Hi Bart,
I agree with the building strategy you propose, but at some point it
stops helping and a bit more attention to detail is needed. Reciprocal
space refinement doesn't seem to do the fine de
mpty - this depends heavily on the choice of radii to determine/shrink
the bulk solvent mask; in such cases, I always calculate a Babinet BS
correction as a control
Best regards,
Dirk.
Am 23.10.10 22:14, schrieb Tim Fenn:
On Sat, 23 Oct 2010 10:05:15 -0700
Pavel Afonine wrote:
Hi Tim,
..
group, resulting in P6_(6-n) (i.e. P6_5 instead of P6_1).
- I wouldn't worry about the mosaicity.
Best regards,
Dirk.
Am 18.10.10 14:03, schrieb Kornelius Zeth:
Dear all,
we have collected S-SAD data (2x4000 Frames, 0.1 degrees, wedges of 40 Frames,
Rf between 3-5% overall) and recei
pointed to two SAXS programs, em2dam and vol2pdb, to
convert low resolution maps into dummy atoms.
Now, I have plenty of options to play with!
Best regards,
Dirk.
Am 13.10.10 13:49, schrieb Dirk Kostrewa:
... maybe, to clarifiy my question a little bit: I want to fill an
essentially flat cr
Best regards,
Dirk.
Am 13.10.10 13:00, schrieb Dirk Kostrewa:
Dear CCP4ers,
is there a program around that allows to fill an input map or mask
with dummy atoms?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.0
Dear CCP4ers,
is there a program around that allows to fill an input map or mask with
dummy atoms?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
ith a sum over
your compound atoms. The Crick-Magdoff equations has been recently
discussed on this board:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg10039.html
Good luck,
Dirk.
Am 29.09.10 09:09, schrieb intekhab alam:
Hi Folks
I have a query regarding the difference map between th
umber of observations.
Interestingly, in your Acta Cryst paper, restraints are also counted as
observations (for instance, in Table 1 and §2.3), but in the derived
residuals and ratios, it's clear that they reduce the effective number
of parameters.
Best regards,
Dirk.
Am 20.09.10 13:2
gards,
Dirk.
The complication is that a 'weak' restraint is equivalent to less than
1 parameter (I call it the 'effective no of restraints': it can be
calculated from the chi-squared for the restraint). Obviously no
restraint is equivalent no parameter, so you can think of i
Dear Ian,
Am 17.09.10 12:30, schrieb Ian Tickle:
Dirk
Personally I wouldn't make use of the deposited Fcalcs, I would insist
on having the refined model, not only for the reasons Pavel gave, but
also because it's never clear which mathematical model was used to
produce the deposi
Hi Pavel,
Am 16.09.10 17:56, schrieb Pavel Afonine:
Hi Dirk,
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final
ution?
The final Fcalc are our best model and can be used to reproduce the
final statistics (which would remove the sfcheck annoyance) and to
reproduce the final electron density maps, and the coordinates can be
used for what ever purpose they are needed, irrespective of a
als failed.
Good luck,
Dirk.
Am 13.09.10 16:52, schrieb Paul Holland:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high sequence similarity to the search model with several predicted flexible
loop regions; however, all attempts
register of at least some side chains either in the 2mfodfc-map
or in one of the real-space-averaged 2mfodfc-maps.
Good luck,
Dirk.
Am 01.09.10 17:12, schrieb Roger Rowlett:
I am trying to find a MR solution for a large unit cell (R3:H,
158x158x196) with a relatively poor, but I think workable search
binding
energy of drug compounds to protein active sites, and estimated that the
errors in the desolvation energies had about the same magnitude as the
total net binding energy. So, this is another big source of inaccuracy,
especially with very different drug compounds.
Best regards,
Dirk.
Am
... yes, and this is the reason why sfcheck should be replaced by a
more modern program at the Protein Data Bank!
Best regards,
Dirk.
Am 13.07.10 22:15, schrieb Ethan Merritt:
Should be in an FAQ somewhere:
Q: Why does sfcheck not reproduce my original R factors?
A: Because instead of using
, you
find a colleague at your institute to help you with that.
Good luck,
Dirk.
Am 13.07.10 14:32, schrieb James Whittle:
Hi all-
I'm trying to convert a cryoEM map from FREALIGN for use with various
CCP4 programs, or with MAPMAN. Even though the MRC format is derived
from the CCP
Hi Tom,
very nice tool! It would be good to get numerical values of the plotted
distributions as well, like mean, median, standard deviation and so on.
Best regards,
Dirk.
Am 08.07.10 15:20, schrieb Tom Oldfield:
Sampath
With regard to your question on what sort of statistics you should
those from the refinement program.
Annoyingly, I have to discuss/explain this discrepancy in R-factors
every time when I want to deposit a refined X-ray structure with the
Protein Data Bank ...
Best regards,
Dirk.
Am 06.07.10 17:05, schrieb Rakesh Joshi:
Hello,
I refined my structures using
50 A and run a test-refinement.
If this results in more realistic model B-factors, you should have a
closer look at the low resolution data and exclude the ill-measured ones.
Best regards,
Dirk.
Am 30.06.10 19:31, schrieb Vandu Murugan:
Dear all,
If one could find a difference of more
Bill Scott (->Google), and
I've installed the more up-to-date X11 from xquartz.macosforge.org (but
this is not necessary). You may want to try this.
Good luck,
Dirk.
Am 30.06.10 10:48, schrieb Md. Munan Shaik:
Dear BB
I have a problem with coot opening, i tried to open but its not ope
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