t;>>
>>>> Maybe a little plausibility check during cif generation might be
>>>> ok
>>>>
>>>>
>>>>
>>>> Best, BR
>>>>
>>>>
>>>>
>>>> PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact
>>>>
t; Bernhard Rupp
>
> k.-k. Hofkristallamt
>
> Crystallographiae Vindicis Militum Ordo
>
> b...@ruppweb.org
>
> b...@hofkristallamt.org
>
> http://www.ruppweb.org/
>
> ---
>
>
>
>
>
>
>
- --
- --
Dr Tim
chard 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 U
needs to be added externally. 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!
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goet
aw. For Ni the first four planes are (111, 200, 202, 311)
> with 2theta (44, 52, 76, 93 degrees) respectively.
>>>
>>> Why 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
a tool
> that is able to do this that would be based more on structure instead of
> sequence?
>
>
> Thank you in advance for any and all of your replies!
>
>
> Regards,
>
> Ryan Gumpper
>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr
her 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 Grue
.xtrage in attachment.
>
> Thank you so much for your suggestion!
>
>
> ****
>
> Yamei Yu
>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
ute of Advanced Technology (DIAT)
>
> Pune Maharashtra, India
>
> Pin Code-411025
>
> Contact No. Lab.+ 91-20-24304377
>
> Mob: 08698198016
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Description: Digital signature
ation over time? I have SElmet crystals that have
> been lying in a plate for 2 months by now so I was wondering if they are
> still worthwhile the effort of collecting new data from them.
>
> Thank you very much,
>
>
> Maher
--
--
Dr Tim Gruene
Institut fuer anorganische Che
> Department of Oral Biology
> Rutgers school of Dental Medicine
> Rutgers Biomedical and Health Sciences
> Newark, NJ 07103
> USA
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
phases from hkl2map, and wanted to perform
> density modification using Parrot. I used the ha.pdb file I obtained from
> hkl2map to define the atom sites. The program finished and produced two
> possible solutions. Both maps look terrible, far worse than the map
> hkl2map p
but also produced one more positive peak with
> slight movement instead of the negative ball at the bottom (See the figures
> Ion_90, Ion_85, Ion_80). The numbers in the image name represents the
> different occupancy ("100" means 100%, "80" means 80%).
>
>
while average completeness of comparable X-ray data
> sets is 94% (page 21):
> http://phenix-online.org/presentations/latest/2012_afonine_ecm27-final.pdf
>
> All the best, Pavel
>
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG K
ld like to try PrimeX, either for ligand restraint generation or
> refinement, please let me know. Schrödinger offers academic institutions one
> year of free access, which may be renewed on a case-by-case basis.
> Crystallographers at companies will also qualify for a free evaluation trial
od reason to believe the
> compound is in any way chemically modified.
>
> Cheers, Robbie
>
>
>
>> -Original Message- From: Tim Gruene
>> [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Friday, June 13, 2014
>> 13:37 To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK Subje
ngs.
>
> Cheers, Robbie
>
>> -Original Message- From: CCP4 bulletin board
>> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent:
>> Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject:
>> Re: [ccp4bb] Invisible atoms in ligands
>>
&
be captured!)
>
> Cheers phx
>
- --
- --
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 Icedove - http://www.enigmail.net/
iD8DBQF
e libraries we all use just as they do for bugs in the
> programs we all use.
>
> Ethan
> [...]
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Description: OpenPGP digital signature
sionals. Is it a matter of PR between crystallographers and
> other scientists, or does a real problem exist?
>
> Cheers,
>
> Jeff Bell
> PrimeX developer
> Schrödinger, Inc.
>
>
> On Tuesday, June 10, 2014 10:27 AM, Tim Gruene
> wrote:
>
>
>
>
252273 ##
>>>
>>> The discrepancy between numbers for "observations" and "parts"
>>> exactly
>> matches double the number of HKLs with two occurrences in my
>> input file. How could I force treatment of duplicate HKLs as
>> independe
s short and worth considering.
> http://pipeline.corante.com/
>
- --
- --
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 Icedove - http:/
strained refinement. This way the R-factor and R-free
> values have drop 1-2% (before it was 22.3/24.1). The three different
> options suffer from the same problem regarding high B-factors after
> TLSanl. Am I doing something wrong during the TLS refinement? What
> can I do to preserve the
>>>> of
>> technical choices made quite a number of years ago. But good news
>> are that this limitation will be removed in new CCP4 Gui under
>> development.
>>>>
>>>> Eugene
>>>>
>>>> On 3 Jun 2014, at 08:2
take improved resolution cut-off (1.6A, 1.57A), the and CC1/2
> in the outermost shell are lower, and the R-merge,meas,pim are higher. No
> resolution cut-off was used while integrating the data (imosflm), only a mask
> for the beam stop was used.
>
>
> looking forward to yo
oblem? Or is there another
> software instead of baverage I could use to check the temperature factor?
>
> Thanks!
>
> Bing
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Description: OpenPGP digital signature
he purposes of the prevention and detection of crime, ensuring the
> security of our computer systems and checking Compliance with our Code of
> Conduct and Policies.
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
ver, if you deposit
> Fmodel - the total model structure factors Fmodel =
> scale*(Fcalc_atoms + Fbulk_solvent + Fother), then they are your
> model representation in reciprocal space, and in fact, are more
> complete source of information than a bunch of points in a PDB
> file.
&g
m, transbondism,
>
> cisbonding, sizeism, curvature, references to color, alcohol,
> blood, small insects, disgusting cells, and
>
> any combination thereof that may cause symptoms ranging from
> discomfort and anxiety to violent
>
> physical response in sensitive individu
ut every time I
> try to refine again to lower it more, the above happens.
>
> Any suggestions?
>
> Thank you.
>
> Remie
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Vers
y set "2.55 A" as the resolution limit in
> Phenix? Or should I go back to XDS and actually reprocess the data
> with the new limit (2.55 A instead of 2.35 A)?
>
> Thanks,
> Tom
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
tal (20-30%). I have attempted
> chelating away the metal with up to 30 mM EDTA and DFO and then
> dialyzing it away, but this has shown little to no effect. Any
> thoughts or recommendations would be greatly appreciated. Thanks.
>
> Adam
>
- --
- --
Dr Tim Gruene
Institu
AMETER VALUES.
>
> !!! ERROR !!! CANNOT ALLOCATE MEMORY YOU COULD RERUN THIS STEP WITH
> SMALLER VALUES FOR THE PARAMETERS
> NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=
> NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= # command line: #
> xds_par
>
>
- --
- --
Dr
or
> averaged value. Could you please let me know how I can get it. Or
> some other software can determine it. I really appreciate your help
> and response!
>
> Hongshi
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG
licing on the
>>>> good people at the PDB, perhaps the entry page for each
>>>> structure could contain a comments section. Then the
>>>> community could point out serious concerns for the less
>>>> informed users. At least that will give users some
CA
> and assigning alternate positions with HOH and CA in the atom name field
> seems to make trouble for pdb reader software, eg mmdb.
> thanks,
> Alastair Fyfe
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Description: OpenPGP digital signature
; Department of Biochemistry/Redox Biology Center
> University of Nebraska
> N118 Beadle Center
> 1901 Vine Street
> Lincoln, NE 68588
> (402) 472-3626
> mwilso...@unl.edu
>
>
>
>
>
>
> On 5/14/14 11:35 AM, "Tim Gruene" wrote:
>
>> Dear Eri
s not accept liability for any
>> errors or omissions in the contents of this message, which arise as a
>> result of e-mail transmission. If verification is required please request a
>> hard-copy version. Please send us by fax any message containing deadlines
>> as incoming e-mails are not screened for response deadlines. * Employees of
>> the Institute are expressly required not to make defamatory statements and
>> not to infringe or authorize any infringement of copyright or any other
>> legal right by email communications. Any such communication is contrary to
>> Institute policy and outside the scope of the employment of the individual
>> concerned. The Institute will not accept any liability in respect of such
>> communication, and the employee responsible will be personally liable for
>> any damages or other liability arising. Employees who receive such an email
>> must notify their supervisor immediately. *--
>>
>
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Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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to make
>> defamatory
>> statements and not to infringe or authorize any infringement of copyright
>> or any other legal right by email communications. Any such communication
>> is contrary to Institute policy and outside the scope of the employment
>> of
>> the individual concerned. The Institute will not accept any liability in
>> respect of such communication, and the employee responsible will be
>> personally liable for any damages or other liability arising. Employees
>> who receive such an email must notify their supervisor immediately.
>> --
>>
>>
>>
>>
>>
>> --
>> Dr Jon Agirre
>> York Structural Biology Laboratory / Department of Chemistry
>> University of York, Heslington, YO10 5DD, York, England
>> http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
>> +44 (0) 1904 32 8253
>>
>>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
Department of Molecular
> Microbiology and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica F, co-editor
>
> e-mail: mbfro...@post.tau.ac.il
> Tel: ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
>
> On May 13, 2014, at 10:38 ,
.nsls.bnl.gov/
>>> Photon Sciences and Biosciences Dept
>>> Office and mail, Bldg 745, a.k.a. LOB-5
>>> Brookhaven Nat'l Lab. Phones:
>>> Upton, NY 11973631 344 3401 (Office)
>>> U.S.A. 631 344 2741 (Facsimile)
>>> =
>>>
>>
>>
>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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>The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> **
>Little known gastromathematical curiosity: let "z" be the
>radius and "a" the thickness of a pizza. Then the volume
> of that pizza is equal to pi*z*z*a !
> **
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
ile /tmp/hbotti/COMP-N-TcG6PDH_30_1_pdb.tmp has been read in.
> Read in 15722 atoms from XYZIN2
>
> XYZIN2 will be appended to XYZIN1 keeping constituent chains separate.
>
> Checking for duplication of chain A
> ... replacing duplicated chain ID A by new_chain_id E
> Checking for duplication of chain B
> ... replacing duplicated chain ID B by new_chain_id F
> Checking for duplication of chain C
> ... replacing duplicated chain ID C by new_chain_id G
> Checking for duplication of chain D
> ... replacing duplicated chain ID D by new_chain_id H
> Some chains from XYZIN2 renamed.
>
> Times: User: 0.2s System:0.0s Elapsed: 0:00
>
> #CCP4I TERMINATION STATUS 1
> #CCP4I TERMINATION TIME 09 May 2014 09:21:06
> #CCP4I TERMINATION OUTPUT_FILES
> #CCP4I MESSAGE Task completed successfully
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Description: OpenPGP digital signature
use a
> library instead.
>
> openblas/mkl/acml for linear algebra fftw for fourier transform
> sleef for trigonometric functions and other math functions mixmax
> for random numbers And so on...
>
> Pascal
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr.
.@yahoo.com
>>>
>>>
>>>
>>>
>>> On 5/6/2014 11:02 AM, Chris Fage wrote:
>>>> Hi Everyone,
>>>>
>>>> In my 2.5-angstrom structure, there is negative Fo-Fc density
>>>> surrounding a metal ion after refining in
56.1%
> 150017.15 54.8%96.9*-20.745 633
> 3.08 14177 704 725 97.1% 114.8%124.6%
> 141652.95117.7%87.5*-30.632 637
> total 990754506 4598 98.0% 9.3% 9.5%
w.r.t. the refined occupancy.
Best,
Tim
On 05/07/2014 06:01 PM, Edward A. Berry wrote:
> On 05/07/2014 10:52 AM, Tim Gruene wrote:
>> At 2.5A resolution (the resolution this thread is about)
>
> But maps ae not made "at 2.5 A" but from say 30A to 2.5 A. In
> princi
d reduce the number of electrons. I always assumed
> they only would get distributed differently.
>
> Best, Herman
>
>
>
> -Ursprüngliche Nachricht----- Von: CCP4 bulletin board
> [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tim Gruene Gesendet:
> Mittwoch, 7. Ma
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
P.S.: For clarity, I meant to say 'calculate' (with full-matrix
refinement) instead of 'collect'.
Tim
On 05/07/2014 04:52 PM, Tim Gruene wrote:
> Dear Bernhard,
>
> I just happen to collect the correlation betw
after refining in Phenix. From anomalous
> diffraction I am certain of the metal's identity and position in
> each monomer. Also, the ion is appropriately coordinated by nearby
> side chains. Should I be refining the occupancy of the ion in
> attempt to "flatten" the negative
ver the rest of the software train that produced the
> images I once made?
>
> Or alternately how to create a similar view using pymol?
>
> Many thanks,
>
> Charlie
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
r the drop is set but unfortunately they
> dissolve overnight. The plate is kept at 16 degree.
>
> Could anyone elaborate on this. Is it possibly occurring because
> Adenosine has stability issues.
>
> Thanks for your suggestions. ~ Maria
>
- --
- --
Dr Tim Gruene
Institut fuer
now, I want to use the phenix to refine a complex structure. But I
> found that I cannot get the ligand cif file from the CCP4 search.
> The ligand is dibenzothiophene. So do you have any idea to help me.
> Thanks very much for your help. Best wishes.
>
>
>
>
> Robert
ago, before the advent of Pilatus detectors, that the
>>> best strategy was a sort of compromise between number of images and
>>> detector readout noise "overhead." I have heard that Pilatus detectors,
>>> however, have essentially no readout noise, so I am wondering whether
>>> strategies have changed in light of this, i.e., is the best practice now to
>>> collect as many images as possible at lowest exposure possible?
>>>
>>> JPK
>>>
>>> ***
>>> Jacob Pearson Keller, PhD
>>> Looger Lab/HHMI Janelia Farms Research Campus
>>> 19700 Helix Dr, Ashburn, VA 20147
>>> email: kell...@janelia.hhmi.org
>>> ***
>>>
>>
>> Harry
>> --
>> ** note change of address **
>> Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick
>> Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
>> Chairman of European Crystallographic Association SIG9 (Crystallographic
>> Computing)
>>
>>
>>
>>
>>
>>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
ror, please notify us immediately.
> Thank you for your cooperation.
>
- --
- --
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: Us
procedure to activate ShelxCDE on CCp4
> interface and it worked. But this time its not working.
>
> Please suggest me how to solve this issue.
>
> Thanking you in advance.
>
>
>
>
>
>
>
> Best regards
>
> Shanti Pal
>
- --
- --
Dr Tim
30/2014 01:31 AM, Cygler, Miroslaw wrote:
> Hi, I have shelx programs installed on my computer but only shelxs
> shows as active on the ccp4i interface. How to activate shelxCDE?
> Thanks,
>
> Mirek
>
>
>
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Ch
>>
>>>>
>>>> I had run imosflm successfully just 2 hours before this
>>>> instance.
>> After that, I had enabled the older version of CCP4-6.3 (by
>> sourcing it from the .bashrc file) for sometime to look at the
>>
all ??...
>>
>> Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.8 - 3.6 - 3.4 - 3.2 - 3.0 - 2.8 -
>> 2.60
>> N(data) 375 493 580 1319 450 538 679 866 1081 1414 1709
>> 58.8 38.6 32.6 38.3 27.7 27.2 21.9 18.4 12.6 9.5 6.1
>> %Complet
synchrotrons, I
> guess for FELs it's different, i.e. much greater coherence length?
> This relates to a question I asked on the BB some time ago: if the
> coherence length is long enough would you start to see the effects
> of interference in twinned crystals, i.e. would the summat
on cutoff at for example 3.8 Å for substructure determination
> with an *E* min value of for example 1.6 to search for X no. of protein
> sulfur sites.
>
> Thanx in advance
> Monica
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key
eposition? (In this case
> the resolution is quite high.)
>
> Thanks.
>
> Bill
>
>
>
>
>
> William G. Scott
>
> Contact info: http://chemistry.ucsc.edu/~wgscott/
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
s but no TLS records
> (resolution=3.30A). Please send us the TLS records."
>
> I want to know how to generate this TLS records.
>
>
> Thanks in advance.
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
have never tried that myself.
>
> And if you run the refmac, and the pdb that is generated does not
> show the description of your link that means that the description
> of your link is not right.
>
> Hope this helped.
>
> Meisam
>
- --
- --
Dr Tim Gruene
Institut fuer anorgani
esolution one was re-refined without
>> that targeting.
>>
>> Gerard.
>>
>> --
>> On Fri, Apr 04, 2014 at 04:55:03PM +0100, Gerard Bricogne wrote:
>>> Dear Nat and Tim,
>>>
>>> On Fri, Apr 04, 2014 at 08:18:06AM -0700, Nat Echols wrot
4/2014 11:49 AM, saleem raza wrote:
> Hi, I was wondering if anyone can help me with the installation of
> xds on iMac? regardsSaleem
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Ver
ld anyone please explain about this!
>
> Sincerely, S.M. Jaimohan, Ph. D
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BE
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
ould be made more clear in the second
> edition of the offending side bar (where regurgitations of
> Wikipedia usually don't cut it). In this instance more accuracy at
> the expense of some parsimony can be justified.
>
> Cheers, BR
>
> -Original Message- From: Tim G
ote:
> On 2 April 2014 12:49, Tim Gruene wrote:
>
>> P.S.: complex numbers together with the operation '+' defined in
>> the canonical way fulfill the axioms of a vector space, hence
>> complex number are vectors. If you also take the operation '*'
>
d you please define the vector products
> for complex numbers?
>
> Thx, BR
>
- --
- --
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
hese quantities add up to the Structure Factor F(s), I
> guess I'm really asking what a structure factor is. Rupp says a
> structure fator is a vector "representing" the diffracted X-rays",
> which i take to be consistent with this if vector is in the
> complex pl
es not depend - the rotation matrices are a representation
of the group SO(3) and hence the matrix multiplication is associative.
It does not matter whether you start left or right or in the middle -
that is not the same as not being commutative.
Cheers,
Tim
--
Dr Tim Gruene
Institut fuer anor
s above" #CCP4I TERMINATION TIME 26 Mar 2014
> 18:50:58 #CCP4I MESSAGE Task failed
>
>
> Any help would be greatly appreciated!
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-
> program?
>
> Thank you very much!
>
> Best wishes,
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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27;m sure I could write a
> wrapper script of my own, but I was trying to avoid reinventing the
> wheel.
>
> Eric
>
>
> On Wed, Mar 26, 2014 at 5:51 AM, Tim Gruene
> wrote:
>
> Dear Eric,
>
> I usually use cif2mtz from CCP4 to import structure factor files
> f
export: Command not found. export: Command not found.
> export: Command not found. if: Expression Syntax.
>
> Output File Name = 2hr0-sf.mtz : (MTZ format)
>
> No output file is produced. I recognize some of the output from
> ccp4-setup.sh, but I don't know what's go
y and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica F, co-editor
>
> e-mail: mbfro...@post.tau.ac.il
> Tel: ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
>
> On Mar 25, 2014, at 10:26 , Tim Gruene wrote:
>
>
anything
>> in the range from "won't work" to "use software X to analyze data in
>> space group P-43N" would be welcome.
>>
>> Thanks.
>>
>>
>> Andreas
>>
>>
>>
>>
>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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diffraction on campus.
>
> I would very much appreciate advice on how to deal with this, anything
> in the range from "won't work" to "use software X to analyze data in
> space group P-43N" would be welcome.
>
> Thanks.
>
>
> Andreas
>
>
efault it
> will scale them to together first, but you can skip that if you
> want
>
> It might not scale well to a large number of files (OK up to about
> 10 I guess)
>
> Phil
>
> On 14 Mar 2014, at 09:33, Tim Gruene
> wrote:
>
> Dear all,
>
> I
dealt with automatically.
Regards,
Tim
On Fri, Mar 21, 2014 at 08:40:44AM -0600, Aaron Greenwood wrote:
> Thanks,
>
> Aaron Greenwood
>
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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!?
Best,
Tim
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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iD8DBQFTIszcUxlJ7aRr7hoRApYyAKDt36pF11DAbkfcXVq
ppreciated. Thanks in advance.
>
> Kok Lian
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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Commen
file or directory
>
>
> With xdsstat, it complains:
>
> xdsstat: Cannot open environ.def
>
> It seems that one needs to set up a CCP4 environment in order to
> run xds in linux.
>
> I have ccp4 (the latest vision for linux) installed. And I use
> Ubuntu 12.04 LTS
gt;> of ligand molecules and water, there is a good Fo-Fc map (above 3 sigma),
>> devoid of any 2Fo-Fc map.
>>
>> 1.What does it physically mean and why the 2Fo-Fc map was not generated
>> properly?
>>
>>
>>
>> 2. Can we fit ligand molecule ther
t cases, but
> it might be important in others...
>
> All the best,
>
> Jacob Keller
>
>
> *** Jacob Pearson Keller,
> PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr,
> Ashburn, VA 20147 email: kell...@janelia.h
t; *Department of Atomic Energy(Govt.Of India)*
> *ACTREC TATA Memorial Center *
> *Kharghar Navi-Mumbai*
> *Mumbai-410210*
> *India*
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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mer in the crystal structure.
>
> Does any of you know other examples? Thank you so much!
>
> Best, Wei
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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-BEGIN PGP SIGNATURE-
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piler to non-existent gcc-4.2.1, so it
>> doesn't work.
>>
>> Do you have a reason to build CCP4 from source? There are binaries
>> available for OSX.
>>
>> Best regards
>> Marcin
>>
>
- --
- --
Dr Tim Gruene
Institut fuer anor
spect to the initial
> structure after superimposition.
> thank you all in advance
>
> Regards
>
> *Rajan kumar choudhary*
> *Senior Research Fellow*
> *Department of Atomic Energy(Govt.Of India)*
> *ACTREC TATA Memorial Center *
> *Kharghar Navi-Mumbai*
> *Mumbai-4
> oils.In silicon oil there was immediate precipitation, but none in
> parafin oil.
>
>
> Prerana
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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Version: GnuPG v1.4.12 (GNU/Linu
t; larger). The cif dictionary for _exptl_absorpt_correction_T_
> states "The permitted range is 0.0 -> 1.0", which clearly has to be
> a different definition.
>
> Any pointers are welcome,
>
> Cheers,
>
> Jens
>
- --
- --
Dr Tim Gruene
Institut fuer an
;>> I have done the molecular replacement using the domains of the
>>> molecules separately, now I have to put all together, however
>>> they have a different symmetry.
>>>
>>>
>>> I will appreciate any kind of help.
>>>
>>>
>>>
>&g
so
> tried with and without sigma weight, but nothing changed again.
> "external harmonic" restraints worked for protein parts.
>
> I would appreciate any suggestions and comments. Thank you so much
> in advance,
>
> Koji
>
- --
- --
Dr Tim Gruene
Institut fu
f help.
>
>
> Regards,
>
>
>
> Mnika
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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>>>> Van: Paul Emsley Verzonden: 12-2-2014 19:23 Aan:
>>>> CCP4BB@JISCMAIL.AC.UK Onderwerp: Re: [ccp4bb] Sister CCPs
>>>>
>>>>
>>>> On 12/02/14 15:59, George Sheldrick wrote:
>>>>
>>>> It would be so nice to have
__
>
>
Derek Logan tel: +46 46 222 1443
> Associate Professor mob: +46 76
> 8585 707 Dept. of Biochemistry and Structural Biology
> www.cmps.lu.se<http://www.cmps.lu.se> Centre for Mol
phate..
>
> Thanks in advance
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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iD8DB
chricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tim
> Gruene
> Gesendet: Donnerstag, 13. Februar 2014 16:22
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] create a lower resolution data set by truncating a high
> resolution data
>
>
>>>>
>>>> FWIW, the remit of CCP4BB, held at jiscmail-central, is describes as:
>>>>
>>>> /The CCP4BB mailing list is for discussions on the use of the CCP4
>>>> suite, and macromolecular crystallography in general./
>>>>
>>>>
>>>>
>>>> Thus wet-lab questions are not off-topic (not that anyone recently
>>>> described them as such).
>>>>
>>>> Having said that, Jiscmail mailing lists are easy to set-up (providing
>>>> that you can reasonably expect that the mailing list will improve
>>>> knowledge sharing within the UK centered academic community) and
>>>> relatively low maintenance. I, for one, would not be entirely unhappy to
>>>> miss out on questions about lysis.
>>>>
>>>> Paul.
>>
>>
>>
>>
>> --
>> Dr Eugene Valkov
>>
>> Room 3N049
>> Division of Structural Studies
>>
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue
>> Cambridge Biomedical Campus
>> Cambridge CB2 0QH, U.K.
>>
>> Email: eval...@mrc-lmb.cam.ac.uk
>> Tel: +44 (0) 1223 267358
>>
>
>
>
> -
> Francis E. Reyes PhD
> 215 UCB
> University of Colorado at Boulder
> --
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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