!
Yamei Yu
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Dr Tim Gruene
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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:
Hi Yamei,
did you by any chance
be based more on structure instead of
sequence?
Thank you in advance for any and all of your replies!
Regards,
Ryan Gumpper​
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doesn't one observe a reflection at, say, 45 degrees?
There will be
a grain oriented in the powder such that x-rays reflect at 45
degrees and so forth. I would expect a continuum of reflections...
thanks for the insight.
Kianoush
- --
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Dr Tim Gruene
Institut fuer anorganische
. The
condition has calcium acetate, peg 4k and sodium acetate buffer.
Unfortunately I am getting oil separation and light ppt. I have no clue
what is wrong. Please help!
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Gillilan wrote:
I have a pdb file for a non-protein having C 1 2/c symmetry. PyMol can't
recognize the spacegroup. Can someone recommend software that can apply the
crystallographic symmetry to give the full structure?
Richard Gillilan
MacCHESS
Cornell University
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Tim Gruene
Institut fuer anorganische Chemie
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iD8DBQFTzk52UxlJ7aRr7hoRAul8AKCHFz/DAoqR7s0fGUp79xx2QlrfCQCeIiiy
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
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-BEGIN
/04/12 10:53, Tom Peat wrote:
Hello Tim,
I believe the notion comes about as one can thread 64 instead of 32 addresses
concurrently, thereby boosting performance. If it has no performance boost,
why would they bother?
Cheers, tom
-Original Message-
From: Tim Gruene [mailto:t
was scaling well
in p321 spacegroup. can anyone explain whats going on?
Thank you very much
Deepthi
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Comment
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iD8DBQFPhFP3UxlJ7aRr7hoRAj4HAKDpHCsN
list.
Cheers,
Tim
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100.00 34.6 34.6
64.83 1.40 H L 4 NONE0.019.0 0 100.00 9.51
9.51 64.83 1.40 I FreeR_flag 5 NONE0.0 311.5 62138
31.1848.8448.84 19.96 2.00 F F 6 NONE0.014.6
62138 31.18 2.11 2.11 19.96 2.00 Q SIGF
- --
- --
Dr Tim
wrote:
I remember reading somewhere (or maybe at a seminar presentation?)
of an agreement between the wwPDB and the CCDC.
I can't find a reference to it on the web - is there such a thing?
Thanks (even lmgtfy answers happily received),
Paul.
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Dr Tim Gruene
Institut fuer
and the cleavage did not work?
Cheers,
Tim
On 04/16/12 09:31, Theresa Hsu wrote:
Dear all
I want to digest a tagged protein with TEV protease, it has
disulfide bridges. Is there any way of doing cleavage without DTT?
Thank you.
Theresa
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Dr Tim Gruene
Institut fuer anorganische Chemie
with SeMet protein.)
Thank you very much for your help! best, Sarah
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Division
__
Lawrence Berkeley National Laboratory * 1 Cyclotron Rd.
Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
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Dr Tim Gruene
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GPG
no installation candidate
is there some other name/link for the package other than the word
coot or do I need to install it by some other method other than
what I have been doing?
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Dr Tim Gruene
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GPG Key ID
purpose. Thank you for your cooperation.
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to do that?Or
can Coot be used to overlap DNA/RNA on their back bone by LSQ or
SSM ? At the same time, are there some software or servers can be
used to search the homology DNA in the database like the Dali
on protein? Thanks in advance! Best wishes leo
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Dr Tim Gruene
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)...plz if anyone is having any idea or trick let me knw.
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doesnt aggregate..doesnt loose activity even after
boiling at 80C.
getting its crystal is important for my thesis. so need help.
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0
3.703 20.519 8.595 1.000 2.22 ATOM 17 Q13 0
0.926 24.359 15.407 1.000 2.33
Thanks,
Kalyan
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coordinates are way different than when the
hydrogens are left in?
Cheers,
Chris
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. Can anybody explain why this is?
It confuses me figuring out which number of reflections to use when
writing tables. I normally use the number from the indexing file.
Is this something related to default parameters in PHENIX?
- --
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr
:35, Jacob Keller wrote:
Well, what about the original DNA fiber diffraction images--no
microcrystals there, as far as I know, but one can clearly see the
stacking distances and the phosphate backbone.
JPK
On Wed, May 9, 2012 at 11:03 AM, Tim Gruene
t...@shelx.uni-ac.gwdg.de wrote:
Dear
a
small hump around 1.5A; I suspect uncertainties in atomic positions
(i.e. the B-factor) reduce the effect. This was consistent in
several other atom-resolution datasets (of different proteins).
I'm curious what the bump around 2.25A is.
-Nat
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Dr Tim Gruene
Institut fuer anorganische
programs give different
alignment results such as from analysis of Clustal W and MULTALIN.
Thanks for any input or comments.
Best regards,
Donghui
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and properly dispose of the e-mail.
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in
the right direction?
Thanks in advance for your help!
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specific
volume?
Many thanks in advance
Eike
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wishes,
Qixu Cai
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long is a piece of string?' in which case resolution values are to
be quoted at CC 1/2 values of 0.2, 0.3, 0.5, 1, etc?
Best wishes,
Michael
Michael Roberts Crysalin Limited Cherwell Innovation Centre 77
Heyford Park Upper Hey ford Oxfordshire OX25 5HD
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Dr Tim Gruene
Institut
thought something like plaque formation but I can't find support
in literature.
All suggestions are welcome!!
Cheers, Anna
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-simple' saved
[111873/111873]
.: 7: build-it-gtk2-simple: not found
anyone know how to fix?
thank you all
Andre
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the
E-value. Is there a search engine that does that? Seems like a
fairly common need, and perhaps I just can't find on PDB website.
Thanks in advance for any suggestions,
Ed.
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images? Thanks! Annette
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with:
sdcorrection norefine scales constant bfactor off reject merge 4
anomalous off
which produces similar results. no merge original index data is
already scaled and Lp-corrected so I want to avoid applying
things twice.
Thanks Phil Jeffrey Princeton
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Dr Tim Gruene
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the initial conditions have been established?
Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
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approach?) Cheers, Alan
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at some level. Then the volume of this blob can
be defined as Vblob = np*Vcell/N, where np is the number of grid
nodes inside the blob.
Pavel
On Fri, Jul 6, 2012 at 7:30 AM, Tim Gruene
t...@shelx.uni-ac.gwdg.de wrote:
Dear Alan,
do you think the notion of 'volume of a peak' makes sense
to download SOMoRe for
molecular replacement?
Thanks in advance
Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza
University of Rome Italy
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-BEGIN PGP
the TO might consider using EPMR, another 6D MR program. The web
site http://www.epmr.info/ seems a lot more up to date ;-)
Cheers,
Tim
On 07/09/12 19:40, James Stroud wrote:
On Jul 9, 2012, at 11:02 AM, Tim Gruene wrote:
Dear Fulvio,
http://lmgtfy.com/?q=somore+molecular+replacement
should
9054 New Zealand Skype:
jtyndall
Ph: +64 3 479 7293
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_chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign SO4 chir_01 S O1 O2
O3negativ
On 11 July 2012 10:59, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Dear Joel,
out of curiosity: what is the Chiral volume outliers issue?
Cheers, Tim
On 07/11/12
' before others. That is
something that should be tested. I have a growing list of chiral
centers that have this problem if you are interested.
Cheers, Robbie
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-BEGIN PGP SIGNATURE
or directory
coot-exe: ./coot-real No core file found. No debugging This is
not helpful. Please turn on core dumps before sending a crash
report
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Dr Tim Gruene
Institut fuer anorganische Chemie
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Building, Rm 310 4500 San Pablo
Road Jacksonville, FL 32224 (904) 953-6372
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not a big deal, but makes comparing secondary structures a bit
more difficult.
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Dr Tim Gruene
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: Jan.Abendroth_at_gmail.com work:
JAbendroth_at_embios.com http://www.emeraldbiostructures.com
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the gauche- conformation of Tyr exists in this
structure. Should I keep it in the final model because there is no
positive map there?
Thank you very much for your input.
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with.
Thanks for comments,
Tim
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Licensee to this
Agreement..
Cheers
-- Ian
On 21 August 2012 10:55, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote: Dear all,
the FCCC license for the program scwrl4
(http://dunbrack.fccc.edu/scwrl4/license/index.html) says that
Licensee will take all reasonable precautions to avoid any
Kharagpur, India.
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iD8DBQFQP1c
know how to convert a .pdf file into a
meaningful Word file. Any suggestions will be greatly appreciated.
The pdf file has numerous figures and tables.
Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
- --
Dr Tim Gruene
Institut fuer
to backtrack
that far, as this data is now very far along in the refinement
process.
Thank you, Michelle Deaton
University of Denver Department of Chemistry and Biochemistry
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Dr Tim Gruene
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regards,
Tim
On 09/05/2012 04:07 PM, Mary Ortmayer wrote:
Hi,
Thanks for your email Ed, here are the log files. Mary
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of transmembrane domain and solublle domain
separately for comparison?
Thank you.
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1.5_22 on my mac to have the COEUS (MIT
software premium). My computer already has java 1.6
How to install the old version. If this old is not on the computer,
then the install commands do not work.
Thanks a lot Subbu
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Dr Tim Gruene
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, the idea is to finally compare to ideal geometry. How should
I generate these values (any softwares in mind)? ANy idea is
welcome. Thanks a lot
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Version
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, and feed my curiosity, too.
Cheers,
Tim
On 09/14/2012 02:39 PM, Ian Tickle wrote:
On 14 September 2012 13:05, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote:
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1
Dear Niu,
as far as I can tell, all your parameters are correct and the
scattering term for f
she sees the same using PointlessScala to get mtz
file, and this has the same effect.
Kind regards,
Inge
Dr. Inge Van Molle Department of Chemistry University of Cambridge
Lensfield Road Cambridge CB2 1EW
Tel 01223330190 iv...@cam.ac.uk
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Dr Tim Gruene
Institut fuer
calculus.
Cheers,
Tim
On 09/14/2012 04:46 PM, Ian Tickle wrote:
On 14 September 2012 15:15, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote:
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1
Hello Ian,
your article describes f(s) as sum of four Gaussians, which is
not the same f(s) from Cromer's
together.
xprep can do this.
Cheers,
Tim
On 09/15/2012 11:10 AM, Rex Palmer wrote:
Is there an easy way to make two .hkl files into one continuous
file?
Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
- --
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Dr Tim Gruene
Institut
-FFTs, it is
formally insensitive to series termination errors. It is only map
calculation where series termination can become a problem.
Thanks to Garib for clearing up that last point for me!
-James Holton
MAD Scientist
On 9/15/2012 3:12 AM, Tim Gruene wrote:
Dear Ian,
provided
-factor refinement significantly improved
R-work and R-free, while maintaining a reasonable gap for lower
resolution models (1.4-1.5 A, around 70,000 reflections). What is
the proper way of modelling the B-factors? Any thoughts and/or
opinions from the community are welcome. Cheers,
- --
Dr Tim
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link
time reference.
It looks like a serious problem. Did I damage the operating
system? Could you please give some advice on how to fix it?
I am anxiously waiting for your help!
Best regards
Jie Liu
- --
Dr Tim Gruene
Institut
Scientist
On 9/18/2012 6:32 AM, Tim Gruene wrote: Hello Oliver,
when you fit the values from ICA Tab 6.1.1.1 with gnuplot, the
values of C and N become much more comparable. c(C) = 0.017 and
especially c(N) = 0.025 0!!! for C: Final set of parameters
Asymptotic Standard Error
termination
errors. It is only map calculation where series termination can
become a problem.
Thanks to Garib for clearing up that last point for me!
-James Holton MAD Scientist
On 9/15/2012 3:12 AM, Tim Gruene wrote:
Dear Ian,
provided that f(s) is given by the formula in the Cromer
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Sorry, 6e^-/A^3 (or -6e/A^3 for charge density people) this should
have said.
On 09/20/2012 11:39 AM, Tim Gruene wrote:
tg@slartibartfast:~/tmp$ phenix.python run.py 0.001 627.413
-4.01639e+06 303880 0.1 275.984
: why should the density be 6A^-3
at the centre of a C atom?
-- Ian
On 20 September 2012 10:39, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote: tg@slartibartfast:~/tmp$ phenix.python run.py 0.001
627.413-4.01639e+06 303880 0.1 275.984
275.247 435.678 0.5
/2012 02:47 PM, Tim Gruene wrote:
Because C has 6 electrons and without thermal vibrations (T=0/B=0)
I thought you'd catch all six of them with a box of 1A side
length.
Is this too simple thinking?
Tim
On 09/20/2012 02:19 PM, Ian Tickle wrote:
Tim, I don't follow your argument: why
suggestions please
Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
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Dr Tim Gruene
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D-37077 Goettingen
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of the information contained in this message is
prohibited.
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is most likely C2221 with
two molecules per ASU (giving around 58% solvent).
Thanks,
Rhys Grinter PhD Candidate University of Glasgow
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clever. One
side effect is that Se-Met residues were left out of the models,
but now Phaser recognises the codes of some modified amino acids
and carries them along.
Best wishes,
Randy Read
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG
anyone
know how to search for structures based on molecular weight. For
example, I want to get a list of all the enzymes (molecular
weight, say, 10kD), is it possible to manage it? Thank you in
advance!
- --
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG
: No such file or directory
Anyone out there knows what to do in order to solve this problem ?
Ta.
F.V.
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using
not be protein
diffraction. I never saw so strange images like this. Does anyone
know what it is? Is it a kind of salt diffraction? Thank you very
much
Chang
- --
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE
I got
the same or nothing. I tried seeding but I had so many crystals
without any improvement. Does anyone have better idea than routine
optimization method in the lab? Thanks in advance.
Jahan
- --
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
, or if there are any tips for fitting residues into
poor density.
Thanks in advance,
Rhys Grinter PhD Candidate University of Glasgow
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU
.
With regards
B. Vijay
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
themselves and within their group. THEY ARE NOT ASHAMED AT
ALL.
This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch
of crooks who are good for nothing but worst for everything.
Sham
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077
and sometimes 0. I am getting the
same result with and without optimization of the X-ray/ADP weight.
Has anyone else noticed that and is there a workaround ?
Demetres
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP
low resolution data, I want use this opportunity
to learn refmac well. So could you please let me know if my doubt
is right regarding SG and how do I troubleshoot.
Thanks
SDY
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iD8DBQFQl5NkUxlJ7aRr7hoRAkUtAKC/6mrt5LdcG9bjZm3rN6UfDzpotQCg7B20
)1273 677512
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iD8DBQFQl6Q
mentioned problem.
For your convenience I have attached the log file of this run.
Thanks is advance.
- --
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU
November 2012 20:29, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote:
Dear,
from the lack of any shelxc-related output in the log-file my
first guess is you don't have shelxc installed on your system - do
you? It is not part of ccp4 and must be installed separately.
(http://shelx.uni
that can be easily identified in the
electron density rather than halide or heavy atom derivatization.
Does anybody have a suggestion for a protein/ligand combination
that could be used for that and that is commercially available?
Thanks!
Uli
- --
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Dr Tim Gruene
Institut
. However,
the one I am currently working on seems to be very picky. If you
have any suggestion regarding to my problems, I will be thankful.
Best regards,
- --
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE
and
extraction of phases. Or will be the same for both..?
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http
: +33
438785494
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
:
Dear all
In *initial screening* using vapor diffusion crystallization, does
it matter whether the reservoir buffer is also the precipitant in
the drop or just a high salt solution like 5 M NaCl?
Thank you.
Theresa
- --
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Dr Tim Gruene
Institut fuer anorganische Chemie
, this will improve their quality, though,
comparing my level of French with my level of English ;-)
Lovely discussion,
Tim
On 11/15/2012 09:15 PM, James Stroud wrote:
On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote:
I have heard this discussion before and reminds me of people
claiming strawberries were
anyone tell me how to do it ?
Rui Wang
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
TERMINATION TIME 19 Nov 2012 16:50:26 #CCP4I MESSAGE Task
failed
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- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http
read on
exactly how to correctly fix this problem.
Thanks, GM
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http
-loading ~/.coot file?
Thank you very much for your help!
Q. Cai
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http
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