Re: [ccp4bb] Add hydrogens

2021-09-29 Thread Tim Gruene
Dear Sam,

refmac5 has the option of 'geometry optimisation', which doesn't
require data. I would assume that you can ask refmac5 to write out the
hydrogen atoms for the resulting PDB file.

Best regards,
Tim

On Wed, 29 Sep 2021 19:03:47 +0800 Sam Tang 
wrote:

> Dear community
> 
> This may appear to be a silly question -- I am trying to add
> hydrogens to the structure in PDB 1CDW. My initial thought is to run
> a single run of refinement with a refinement program. It happens that
> I cannot locate the map coefficients under the entry (am I missing
> something?) So... is there an easy way to do what I want in this case?
> 
> Warm regards
> 
> Sam
> 
> 
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Re: [ccp4bb] criteria to set resolution limit

2021-09-12 Thread Tim Gruene
Dear Farhan,

did you possibly move the detector too far from the crystal, and the
high resolution spots landed on the detector corners? This would
explain the good I/sigma at low completeness. In that case, there is no
reason to discard the data. You detector was simply not large enough to
capture the rest.

Best regards,
Tim

On Sat, 11 Sep 2021 21:25:23 +0530 Syed Farhan Ali
 wrote:

> Dear All,
> 
> I have query regarding one of my dataset. I am running aimless by
> keeping highest resolution 1.62 A and getting  I/SigI = 2 but data
> completeness is around 22 in outermost shell. And if I am increasing
> the resolution cutoff up to 1.8 A then I/SigI is 6.2 and completeness
> is 82.4. I have attached the screenshot of the result.
> What should be the criteria to set the resolution limit?  Should I
> stick to  I/SigI  or I have to consider about the completeness of
> data. And if completeness is also a guiding factor than how much
> minimum completeness I can keep in the higher resolution shell.
> 
> 
> 
> 
> 
> Regards,
> Farhan
> 
> 
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Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

2021-08-30 Thread Tim Gruene
Dear Robbie,

I don't use ccp4 regularly (since our structures are mainly small
molecule structures), but when I do, I often use pdbset. I use it to
remove het-atoms, or side chains, or water molecules, or reset the
B-value.

I also use sftools. I have a script for calculating Rcomplete with
refmac. This script makes use of sftools in the preparation of the
mtz-file.

I use these tools, because they are command line tools - much faster
than GUI based versions.

Best wishes,
Tim

On Thu, 26 Aug 2021 10:29:22 + Robbie Joosten
 wrote:

> Dear CCP4 users,
> 
> We (as in, the CCP4 developers) are investigating some (potentially)
> missing functionality in CCP4i2 and/or Cloud with respect to the
> programs pdbset, pdbcur, coordconv, and sftools. Some of these tools
> are quite old and may need to be replaced by other tools with similar
> functionality. Could you answer a few questions:
> 
> - Do you use any of these tools? 
> - If so, how often? (Few times a week, month, year, or less than once
> a year).
> - Which functionality of program X do you use? 
> - Would you like a graphical interface to that functionality or are
> you happy to use the command line?
> 
> Personal example:
> I use pdbset a few times a month, but only the "noise" function. I
> don't need a graphical interface for it (because it is used in the
> context of pdb-redo). I also use sftools, "reduce -> merge average" a
> few times a year. Again, only from the command line.
> 
> 
> Feel free to send your answers directly to me or to the bulletin
> board if you want to start a discussion. Tips on alternative CCP4
> tools to achieve similar effects are probably also interesting for
> other BB users.
> 
> Cheers,
> Robbie
> 
> 
>  
> 
> 
> 
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Re: [ccp4bb] AI papers in experimental macromolecular structure determination

2021-08-03 Thread Tim Gruene
nt from diffraction image (small molecules):
> Aguiar, J. A., Gong, M. L., Unocic, R. R., Tasdizen, T. & Miller, B.
> D. (2019). Science Advances. 5, eaaw1949.
> 
> Data quality assessment in MX:
> - Vollmar, M., Parkhurst, J. M., Jaques, D., Baslé, A., Murshudov, G.
> N., Waterman, D. G. & Evans, G. (2020). IUCrJ. 7, 342–354.
> 
> Ligand recognition:
> Kowiel, M., Brzezinski, D., Porebski, P. J., Shabalin, I. G.,
> Jaskolski, M. & Minor, W. (2019). Bioinformatics. 35, 452–461.
> 
> Prediction of missing atoms in small molecular structures:
> Thomas, N., Smidt, T., Kearnes, S., Yang, L., Li, L., Kohlhoff, K. &
> Riley, P. (2018).
> 
> ADP estimation (small molecules):
> Gagner, V. A., Jensen, M. & Katona, G. (2021). Mach. Learn.: Sci.
> Technol. 2, 035033.
> 
> 
> --
> Dr. Andrea Thorn | group leader
> andrea.th...@uni-hamburg.de
> 
> Institute for Nanostructure and Solid State Physics, Universität
> Hamburg Luruper Chaussee 149 / Bldg. 610 (HARBOR) | 22761 Hamburg |
> Germany Tel. +49 (0)40 42838 3651
> www.thorn-lab.de<http://www.thorn-lab.de> | www.insidecorona.net
> 
> 
> 
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Re: [ccp4bb] using chooch

2021-07-20 Thread Tim Gruene
Dear Eleanor,

not sure how to make Chooch happy, but maybe Ethan Merrit can make you
happy: there is his excellent server for the anomalous signal for X-ray
scattering at http://skuld.bmsc.washington.edu/scatter/

When you choose Br instead of Grr, you find
http://skuld.bmsc.washington.edu/scatter/data/Br.dat, or you read your
values from the interactive plot
http://skuld.bmsc.washington.edu/scatter/AS_form.html

Best,
Tim


On Tue, 20 Jul 2021 12:28:16 +0100 Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Grr - stuck at home - what is f' and f' for Br???
> 
> All nicely tabulated on my desktop but not here..
> 
> So use chooch..
> but it grumbles about file name null 
> 
> How can I make it happy?
> Any help gratefully received
> 
> Eleanor
> 
> 
> eleanor@wombat cysbfull % chooch -e Br -e 0.92
> ==
>  chooch-5.0.9
>   by Gwyndaf Evans Copyright (C) 1994--2013
>  gwyn...@gwyndafevans.co.uk
> 
> G. Evans & R. F. Pettifer (2001)
>J. Appl. Cryst. 34, 82-86.
> ==
> 
> License information
> ---
> Chooch comes with ABSOLUTELY NO WARRANTY; for details
> type `chooch -w'.  This is free software, and you are
> welcome to redistribute it under certain conditions;
> type `chooch -c' for details.
> 
> You should have received a copy of the GNU General Public License
> along with this program; if not, write to the Free Software
> Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
> 02111-1307, USA.
> 
> -e: Atomic element = Br
> -e: Atomic element = 0.92
> Fluorescence scan filename: (null)
> Chooch output
> 
> 
> 
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Re: [ccp4bb] pictures in emails

2021-07-19 Thread Tim Gruene
Hi Ed, dear ccp4bbs

I fully support your email!

Most email clients have a tick box to include a plain text version in
addition of the html-version in their preferences. 

Reading plain text emails instead of the html-version (which is also an
available option for most email clients) is a very effective barrier
against spam. People should take this into account, considering the
global rise of ransomware attacks, with serious consequences to some
large institutions and companies.

It has always been good netiquette to at least include a text-version
of your email.

Cheers,
Tim

On Sun, 18 Jul 2021 11:17:26 -0400 Edward Berry 
wrote:

> Two suggestions for people sending pictures of electron density to
> the BB:
> 
> 1. Reduce the size of the pictures-
> The two pictures in yesterday's email appear nice and small in my
> email client, but still illustrate what is being described. However
> they are actually 4032x3024 and 2040x1458 pixels, making for rather
> large emails. All that extra resolution is wasted unless the user
> opens the image directly ("view image"), and in any case is
> completely unnecessary for the point being made. I think about
> 600x600 pixels is plenty for almost anything you want to show in
> electron density. This does not require manipulation in photoshop or
> such- just reduce the size of the graphics window and take a
> screenshot of that window.
> 
> 2. send the picture as an attachment rather than inline. That way it
> won't be included in all the replies. Or if the people replying could
> find some way to exclude pictures or formt the reply as plain-text,
> that would help.
> 
> (No, I'm not receiving these emails via 1200 baud modem- but I like
> to save the messages for future reference. If the trend continues
> toward high-resolution inline screenshots, that will take a
> significant amount of disk space. And yes, I know there is an
> archive.) eab
> 
> 
> 
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Re: [ccp4bb] Strange indexing problem

2021-07-05 Thread Tim Gruene
Dear Rob,

at 1.5A resolution, you can comfortably run shelxe. If there is some
useful phase information in your solution, this should complete
your model, remove model bias and the resulting composition might tell
you the proper space group. Rename your PDB-file into 'mymodel.pda'
(pda, not pdb), convert the mtz to 'mymodel.hkl' and run
shelxe mymodel.pda -a10 -s0.4 (where  0.4 corresponds to 40% solvent
model. You don't need to be very accurate).

Good luck,
Tim

On Mon, 5 Jul 2021 13:54:07 + Robert S Phillips  wrote:

> I collected data last week on crystals of tyrosine phenol-lyase
> obtained under new conditions.  The data have higher resolution than
> previous crystals, to 1.5 A.  However, I can't get them to index in
> any space group but P1.  Usually, the space group is P21212.  The
> self-rotation function is attached.  The P1 data will give a
> molecular replacement solution, but it does not refine below 0.46.
> The P1 asymmetric unit fits a dimer, but the assembly is a tetramer.
> In the map, I can see the difference peaks from the other dimer of
> the tetramer.  What could be causing this problem?
> 
> Rob
> 
> Robert S. Phillips
> Professor of Chemistry and of Biochemistry and Molecular Biology
> University of Georgia
> Athens, GA 30602
> Phone: (706) 542-1996
> Fax: (706) 542-9454
> E-mail: rsphill...@chem.uga.edu
> Web:
> http://tryptophan.net<https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab=http%3a%2f%2ftryptophan.net>
> 
> 
> 
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Re: [ccp4bb] How to process two datasets 45 degrees apart?

2021-07-01 Thread Tim Gruene
Dear Murpholino,

in addition to Graeme's explanation w.r.t. XDS, you probably want to
also set the 'STARTING_ANGLE= 90', when you copy  
UNIT_CELL_A-AXIS=
UNIT_CELL_B-AXIS= 
UNIT_CELL_C-AXIS= 
from XDS_ASCII.HKL of the first data set into XDS.INP of the second
one.

Depending on the spacegroup and cell axes, just REFERENCE_DATA_SET=
together with SPACE_GROUP_NUMBER= and UNIT_CELL_CONSTANTS= might be
sufficient.

As a thrid option, you can treat it as one data set and make use of 
EXCLUDE_DATA_RANGE= 46 89 and integrate the data as a single data set.
The latter is probably the most fool proof approach, as long as the
file names for B are numbered 90 to 135.

Best wishes,
Tim


for the second data set
On Wed, 30 Jun 2021 18:57:03 -0500 Murpholino Peligro
 wrote:

> Hi...
> I have a couple of datasets:
> A: From 0 to 45
> B: From 90 to 135
> 
> Can I process them as a unique data set? (with XDS or maybe Mosflm) or
> should I process them apart and then merge them?
> 
> 
> Thanks
> 
> 
> 
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Re: [ccp4bb] Co crystalization with less soluble ligand.

2021-06-23 Thread Tim Gruene
Hi Frank,

heme becomes near completely insoluble when it dimerizes. Fatty acids
are also very insoluble. It is quite hard to get them into HSA, as far
as I remember.

Cheers,
Tim

On Wed, 23 Jun 2021 10:33:42 +0100 Frank von
Delft  wrote:

> And then of course, you need to decide whether you at all care to
> know anything about a compound that is so insoluble that it needs
> that kind of treatment  :)
> 
> On 23/06/2021 09:52, hoh wrote:
> > Hi
> >
> > As total insolubility does not exist, I regularly use another
> > method, which is to deposit a grain of the ligand directly into the
> > drop.
> >
> > In this case, we no longer control the concentration. The goal is
> > to regularly freeze crystals (1 hour, 2 days, 1 week ..). Depending
> > on the results, it is possible to adjust the time. If after one
> > hour, the crystal no longer diffracts, redo the experience by
> > freezing at 10s, 30s, 2mn ..). If a blob appears, frozen after 1
> > week. This technique needs 2 things
> > , time and several exploitable crystals in the drop.
> >
> >
> > FH
> >  
> 
> 
> 
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Re: [ccp4bb] Should Rmerge be reported?

2021-06-10 Thread Tim Gruene
t; 
> 
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> 
> 
> --
> Dr. Manfred S. Weiss
> Macromolecular Crystallography
> Helmholtz-Zentrum Berlin
> Albert-Einstein-Str. 15
> D-12489 Berlin
> Germany
> 
> 
> 
> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
> 
> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
> Forschungszentren e.V.
> 
> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr.
> Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd Rech
> (Sprecher), Prof. Dr. Jan Lüning, Thomas Frederking
> 
> Sitz Berlin, AG Charlottenburg, 89 HRB 5583
> 
> Postadresse:
> Hahn-Meitner-Platz 1
> 14109 Berlin
> Deutschland
> 
> 
> 
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--
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Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] Meaning of a pdb entry

2021-05-31 Thread Tim Gruene
27 May 2021 at 18:34, Hughes, Jonathan
> > mailto:jon.hug...@bot3.bio.uni-giessen.de>>
> > wrote:
> > 
> >  "B = 8π2  where u is the r.m.s. displacement of a scattering
> > center, and <...> denotes time averaging"
> > 
> > Neither of those statements is necessarily correct: u is the
> > _instantaneous_ displacement which of course is constantly changing
> > (on a timescale of the order of femtoseconds) and cannot be
> > measured.  So u2 is the squared instantaneous displacement, 
> > is the mean-squared displacement, and so the root-mean-squared
> > displacement (which of course is amenable to measurement) is
> > sqrt(), not the same thing at all as u.
> > 
> > Incidentally, the 8π2 constant factor comes from
> > Fourier-transforming the Debye-Waller factor expression I mentioned
> > earlier.
> > 
> > Also for crystals at least, the averaging is not only over time,
> > it's over all unit cells, i.e. the displacements are not only
> > thermal in origin but also due to spatial static disorder
> > (instantaneous differences between unit cells).
> > 
> > 
> > it would seem to me that we would be able to interpret things MUCH
> > more easily with u rather than anything derived from u². So then I
> > think what you mean is sqrt() rather than , which seems not
> > unreasonable.
> > 
> > Cheers
> > 
> > -- Ian
> > 
> > 
> > 
> > 
> > 
> > 
> > 
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> --
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> MS 357742,   University of Washington, Seattle 98195-7742
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Re: [ccp4bb] (R)MS

2021-05-27 Thread Tim Gruene
Hello Jon,

Wikipedia has plenty of information on the Debye-Waller factor:
https://en.wikipedia.org/wiki/Debye%E2%80%93Waller_factor

Best,
Tim

On Thu, 27 May 2021 12:25:06 + "Hughes, Jonathan"
 wrote:

> o yes! but maybe the crystal people could explain to me why the B
> factor is the variance (with units of Ų) rather than the standard
> deviation (i.e. RMS, with units of Å) when, to my simple mind, the
> latter would seem be the more appropriate description of variability
> in space? cheers jon
> 
> Von: CCP4 bulletin board  Im Auftrag von
> Pearce, N.M. (Nick) Gesendet: Donnerstag, 27. Mai 2021 12:38
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Analysis of NMR ensembles
> 
> If you want something comparable to B-factors don’t forget to put the
> MSF in the B-factor column, not the RMSF. Will change the scaling of
> the tube radius considerably!
> 
> Nick
> 
> 
> On 27 May 2021, at 11:16, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>
> wrote:
> 
> Cool…
> 
> Purely for visualisation this does look like the approved CCP4 way -
> 
> 
> 
> Harry
> 
> 
> On 27 May 2021, at 10:01, Stuart McNicholas
> <19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk<mailto:19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>>
> wrote:
> 
> Drawing style (right menu in display table) -> Worm scaled by -> Worm
> scaled by NMR variability
> 
> in ccp4mg?
> 
> This changes the size of the worm but not the colour.
> 
> On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>
> wrote:
> 
> 
> Anyway, thanks to all those who answered my original question -
> especially
> 
>Tristan: Chimerax (+ his attached script)
>Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/)
>Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
>Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html)
> and https://www.ccpn.ac.uk/ (of course…) Andrew (uwmn - not sure if
> this is buildable on a modern box) Smita: PyMol (not sure if I’m
> allowed to say that on ccp4bb…)
> 
> or I could script it and use Gesamt or Superpose for the
> superposition if I wanted to stay in the ccp4 universe and had the
> time to spare ;-)
> 
> Harry
> 
> 
> 
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Re: [ccp4bb] weight matrix selection

2021-04-08 Thread Tim Gruene
Dear Luca,

did you click at the empty line below where it says 'automatic'? Maybe
the word 'manual' is just not visible for inappropriate colour settings.

Best wishes,
Tim

On Thu, 8 Apr 2021 18:14:35 +0200 Luca Mazzei 
wrote:

> Dear CCP4 people,
> 
> I am trying to change manually the geometry weight in Refmac, but
> something funny is occurring. As you can see in the snapshot I can
> not switch from auto to manual. Suggestions?
> 
> Thanks in advance,
> 
> Luca
> 
> 
> Luca Mazzei - PhD
> Laboratory of Bioinorganic Chemistry
> Department of Pharmacy and Biotechnology (FaBiT)
> Alma Mater Studiorum - University of Bologna
> Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
> Tel: +39 0512096235
> 
> 
> 
> 
> 
> 
> 
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Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand

2021-04-07 Thread Tim Gruene
Dear Fred,

the error message looks like ligplot was started through a script, that
uses an environment variable, which is not set, soemthing like

${MYLIGPLOTDIR}/components.cif

In case MYLIGPLOTDIR is not set, you would get this sort of error
messages.

Best,
Tim

On Tue, 6 Apr 2021 15:47:21 +0200 Fred Vellieux
 wrote:

> Hi folks,
> 
> I'm trying to run Ligplot on a PDB file that contains a residue with 
> type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 
> years now (which means that I had to reinstall, with an expired
> license, and get familiar with it again). I get the following error
> message (rather cryptic):
> 
> Calling HBADD ...
> Running HBADD
> Het Group Dictionary: /components.cif
> Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb
> Command:  /LigPlus/lib/exe_linux/hbadd 
> /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir 
> /tmp/lig7141158588178475829/
> java.io.IOException: Cannot run program
> "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory
> Other event: state
> 
> Would anyone know what to make out of this message ? Otherwise is
> there another piece of software (called "app" nowadays) that could
> provide me with similar drawings ?
> 
> At some stage I ran PRODRG, introduced the cif file in the file 
> components.cif used by LigPlot (LigPlus). I also replaced the
> coordinate files by those returned by the PRODRG run. Always with the
> same cryptic error message provided by the software (oops, app).
> 
> Thanks,
> 
> Fred.
> 



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Re: [ccp4bb] Maniatis: Molecular Cloning

2021-03-26 Thread Tim Gruene
Dear Aviv, dear Jeroen,

thank you very much for the links to the latest edition! We always
called it 'the Maniatis'...

I was also pointed at "Current Protocols in Molecular Biology", edited
by F. M. Ausubel et al.
https://www.wiley.com/en-us/Current+Protocols+in+Molecular+Biology+-p-9780471503385?purchasedProduct=%2Fen-us%2FCurrent%2BProtocols%2Bin%2BMolecular%2BBiology%2B-p-9780471503385#
as an alternative

Best regards,
Tim

On Fri, 26 Mar 2021 13:11:08 +
Aviv Paz  wrote:

> Dear Tim,
> 
> Here is a link to the new version (with some author changes):
> https://www.cshlpress.com/default.tpl?cart=1616763922770582099=T=full=oop_title&--eqSKUdatarq=934
> 
> All the best,
> 
> Aviv Paz, Ph.D.
> Associate Research Scientist | Hauptman-Woodward Medical Research
> Institute Adjunct Associate Professor of Oncology | Roswell Park
> Comprehensive Cancer Center p: +1 716 898 8619 | f: +1 716 898 8660
> e: a...@hwi.buffalo.edu
> Hauptman-Woodward Medical Research Institute
> 700 Ellicott Street | Buffalo, NY 14203-1102
> hwi.buffalo.edu
> 
> 
> 
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[ccp4bb] Maniatis: Molecular Cloning

2021-03-26 Thread Tim Gruene
Hello erveryone,

does anyone know whether Maniatis/Fritsch/Sambrock "Molecular Cloning"
are still being printed and sold? I could not find it by ISBN
(0‐87969‐309‐6) at my favourite book store.

Or is there anything comparable?

Best regards,
Tim

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Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

2021-02-20 Thread Tim Gruene
Hi Matthias,

I have been using Debian for more than a decade. Every stable release
is supported for at least 5 years. 
Many crystallographic libraries and some programs are part of the
standard repository, like raster3d, pymol, shelxle, libccp4,
libclipper, ...

Debian is particularly stable, and requires little maintenance. 

Cheers,
Tim

On Fri, 19 Feb 2021 21:35:46 +0100
Matthias Zeug  wrote:

> Hi all,
> 
> 
> 
> I just came across the (already quite old) news that Red-Hat switches
> their support-policy for CentOS to a rolling preview model (replacing
> CentOS Linux by CentOS Stream):
> 
> https://www.zdnet.com/article/why-red-hat-dumped-centos-for-centos-stream/
> 
> https://www.enterpriseai.news/2021/01/22/red-hats-disruption-of-centos-unlea
> shes-storm-of-dissent/
> 
> 
> 
> I wondered if that has any implications for the community, as
> scientific programs - maybe except the big ones like coot, Phenix,
> and ccp4 - are often not *that* well maintained for an extended
> period. I had the impression CentOS was liked especially for its
> "unbreakability,"  and it seems to be the main developing platform
> for some widely used smaller programs (e.g., adxv).
> 
> 
> 
> Do you think it would be advisable to switch to a Ubuntu-distro when
> setting up new workstations in the future, or is it safe to stick to
> CentOS?
> 
> 
> 
> Please let me know what you think :-)
> 
> 
> 
> Best,
> 
> 
> 
> Matthias
> 
> 
> 
> 
> 
> Matthias Zeug
> 
> Buchmann Institute of Molecular Life Sciences
> 
> Goethe University Frankfurt
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-19 Thread Tim Gruene
Dear Jacob,

you cannot kill a virus. It is not alive, but a complex chemical
compound that interferes with the chemistry of the host. So why don't
you work on the part of your conept over the week-end and present the
concept?

Cheers,
Tim


On Fri, 19 Feb 2021 12:55:32 -0500 Jacob Keller
 wrote:

> I don't think seeing the big picture resolves, or even addresses, the
> question of possibly using a live vaccine. Some big-picture
> considerations favor each side.
> 
> The concern of mutation is a grave one, and an unknown. I would point
> out, however, that the same considerations apply to the wild virus
> currently scourging the planet (well, and every other virus currently
> slinking around the biome). The distinction would be, I guess, that
> we would be actively contributing in some way. On the other hand,
> maybe being passive is like not throwing a rope to a drowning man?
> 
> Maybe having a "v-day" would address this: introduce the
> virus-vaccine at well-chosen locations, aka super-spreader events,
> which, like well-placed demolition dynamite, would cause a "flash
> pan-infection." Funnily, this would require all of the pandemic rules
> to be turned on their heads! Presumably this generates herd immunity
> within a couple of weeks, as well as its fair share of adverse
> reactions and deaths. As a safety measure, have two orthogonal
> chemical kill switches based on plentiful inexpensive well-tolerated
> compounds, say a vitamin or pesticide (yes, pesticide, that stuff
> that's always sprayed all over your food). Use those to quench the
> vaccine before mutation, say 6-8 wks. Then, back to normal life, and
> start honing similar tools for coming pandemics, a "holohomoimmune
> system."
> 
> Here's a question to the informed-consent hawks: would exposing
> everybody to the virus while providing two compounds to block
> completely the effects be considered a valid opt-in/out? Or what if
> the default was switched, such that both compounds were required for
> infection, and therefore one had to actively opt in?
> 
> I don't know--it seems that many of the objections to the idea are
> based on the bioethical concept "first do no harm," but that
> principle is not necessarily adopted in all cases.
> 
> One of the best things I learned in med school:
> 
> Medicine is, fundamentally, "uncertainty management:"
> 
> there are almost never any certainties in medicine, and one has to
> use a Bayesian framework and a few bioethical principles to figure
> out what to do next.
> 
> Anyway, rest assured, I have not yet ordered the primers for creating
> such a virus-vaccine...
> 
> All the best, and have a good weekend everyone,
> 
> Jacob
> 
> 
> 
> On Fri, Feb 19, 2021 at 5:54 AM Robbie Joosten
>  wrote:
> 
> > Hi Tim,
> >
> > Very good points. The big picture is hard to grasp and we end up
> > taking political choices rather than anything else. I'm very glad
> > that we can outsource these choices to others every four year here.
> >
> > Lockdowns may save lives in the here and now, but the global
> > economic damage makes life for others much harder to a point that
> > it may actually kill them. Economic decline in the First World may
> > be something with which that we can deal but, like viruses, it
> > blows over to other parts of the world where economic growth is the
> > real life saver. Does the prolonging of a reasonably measurable
> > number well-lived lives in the West outweigh the extinguishing of a
> > hard-to-assess number of much younger lives in the rest of the
> > world? I'm glad I don't have to make that call.
> >
> > Cheers,
> > Robbie
> >  
> > > -Original Message-
> > > From: CCP4 bulletin board  On Behalf Of Tim
> > > Gruene
> > > Sent: Friday, February 19, 2021 09:33
> > > To: CCP4BB@JISCMAIL.AC.UK
> > > Subject: Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"
> > >
> > > Hi Jessica,
> > >
> > > one comment: death cannot be prevented. It is a certainty as soon
> > > as you are born (well, 9 months before).
> > >
> > > While this seems an obvious subtlety, many of the current
> > > measures seems to be influenced by the (probably unconscious)
> > > belief one can defeat  
> > death.  
> > > We can only reduce the risk to die at a certain moment and of a
> > > certain cause.
> > >
> > > The example of rabbits in Australia also illustrates how simple
> > > minded humans generally are: we focus on one thing, but usually
> > > fail to take a  
> > l

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-19 Thread Tim Gruene
just have to take it easy
> >> until herd immunity is established, even though few million
> >> grandparents will die in the process while the rest of us enjoy
> >> indoor dining.
> >>
> >>
> >>
> >> On Wed, Feb 17, 2021 at 12:33 PM Jacob Keller
> >>  wrote:
> >>  
> >>> It would seem to me that it should be possible to generate
> >>> versions of the Covid virus that would:
> >>>
> >>> A. be extremely contagious and yet
> >>> B. be clinically benign, and
> >>> C. confer immunity to the original covid virus.
> >>>
> >>> If, then, this virus could be released, with appropriate "kill
> >>> switch" safeguards built in, would this not solve the world's
> >>> pandemic problems? Is there any reason, practically, why this
> >>> approach would not be feasible?
> >>>
> >>> Maybe we don't really know enough to manipulate A, B, C yet?
> >>>
> >>> Or maybe it's too scary for primetime...nightmare bio-warfare
> >>> apocalypse?
> >>>
> >>> Has this sort of thing been done, or does it have a name?
> >>>
> >>> Jacob
> >>> --
> >>>
> >>> +
> >>>
> >>> Jacob Pearson Keller
> >>>
> >>> Assistant Professor
> >>>
> >>> Department of Pharmacology and Molecular Therapeutics
> >>>
> >>> Uniformed Services University
> >>>
> >>> 4301 Jones Bridge Road
> >>>
> >>> Bethesda MD 20814
> >>>
> >>> jacob.kel...@usuhs.edu; jacobpkel...@gmail.com
> >>>
> >>> Cell: (301)592-7004
> >>>
> >>> +
> >>>
> >>> --
> >>>
> >>> To unsubscribe from the CCP4BB list, click the following link:
> >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>>  
> >>
> >> --
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>  
> >
> >
> > --
> >  patr...@douglas.co.ukDouglas Instruments Ltd.
> >  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
> >  Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek
> >
> >  http://www.douglas.co.uk
> >  Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
> >  Regd. England 2177994, VAT Reg. GB 480 7371 36
> >
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Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-17 Thread Tim Gruene
Hi Jacob,

how do you think this should be possible? In order to infect others,
the virus particle needs to proliferate (that's the only thing it
does). It profilerates by hijacking the machinery of one cell of your
body and turn it into a virus factory. Your body does not like this
abuse and kills the cell, and also tries to kill the virus particles.
The virus does not make you sick, it only captures one cell. The
reaction of your body to kick out the virus, and the cell that does not
do it's job anymore, make you sick. A and B are mutually exclusive. B +
C is named vaccine.

Best,
Tim


On Wed, 17 Feb 2021 12:33:09 -0500 Jacob Keller
 wrote:

> It would seem to me that it should be possible to generate versions
> of the Covid virus that would:
> 
> A. be extremely contagious and yet
> B. be clinically benign, and
> C. confer immunity to the original covid virus.
> 
> If, then, this virus could be released, with appropriate "kill switch"
> safeguards built in, would this not solve the world's pandemic
> problems? Is there any reason, practically, why this approach would
> not be feasible?
> 
> Maybe we don't really know enough to manipulate A, B, C yet?
> 
> Or maybe it's too scary for primetime...nightmare bio-warfare
> apocalypse?
> 
> Has this sort of thing been done, or does it have a name?
> 
> Jacob



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Re: [ccp4bb] RCrane in Coot 0.8.9.2 for Mac

2021-02-09 Thread Tim Gruene
Hi Almudena,

in my Coot 0.9.2, the Calculate menu has the entry 'RCrane launch' as
second last subentry. 

Best,
Tim


On Tue, 9 Feb 2021 13:43:25 + Paul Emsley
 wrote:

> On 09/02/2021 13:33, Almudena Ponce Salvatierra wrote:
> > 
> > I have Coot 0.8.9.2 installed on macOS Catalina. I would like to
> > launch RCrane, but I can't find it under "Extensions".
> > 
> > Does anybody know whether there is a way I can make it work on the
> > version of Coot, or should I rather uninstall it and look for
> > another one?  
> 
> Hi Almudena,
> 
> I consulted the release notes, and it says that RCrane was restored
> in 0.8.9.2, so the fact that you can't find it is perplexing. Maybe
> it moved (I don't recall now, it's been a while).
> 
> Maybe you can find it in a more recent version? (although you might
> find that other things have moved).
> 
> Paul.
> 
> 
> 
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Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

2021-01-04 Thread Tim Gruene
Dear Andreas,

the eiger2cbf code also contains a plugin. I have been using it for
at least 2 years with the LIB= keywords in XDS.

The compilation is not automatically switched on with the Makefile, but
it takes very litte adjustment to create the binary plugin-worker and
the plugin plugin.so

It works greatly.

Best,
Tim

On Mon, 4 Jan 2021 11:10:34 +0100 Andreas Förster
 wrote:

> Dear Graeme, all,
> 
> to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to
> process EIGER and EIGER2 data collected at the synchrotron, Herbert
> Bernstein created a Windows installer for Takanori Nakane's eiger2cbf
> converter.  You can find it here:
> https://github.com/nsls-ii-mx/eiger2cbf.  Documentation is at the
> very bottom.  It works for CAP.  I haven't tried to see how useful it
> is in other contexts.  It's a converter, not a plugin, but it lets
> you work with HDF5 data under Windows.
> 
> All best.
> 
> Andreas
> 
> 
> 
> On Mon, Jan 4, 2021 at 10:22 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
> graeme.win...@diamond.ac.uk> wrote:  
> 
> > Hi All,
> >
> > Sorry for the slow response - holiday season & all (I am sure many
> > of us needed a break at the end of 2020)
> >
> > Windows is currently not super well supported for xia2 / DIALS work
> > and won’t work at all for xia2 / XDS for the simple reason that XDS
> > is not available for the platform (hence absence of durin plugin
> > for Windows mentioned elsewhere in this thread)
> >
> > Your data are from 2019 I would guess from the log text
> >
> > In this case I would honestly suggest that the best method to
> > process this data is to either -
> >  - work on a UNIX based system
> > or
> >  - restage the data to Diamond and process there
> >
> > I’m happy to help (off list) with the details of this if it would
> > help
> >
> > We probably should invest some effort in properly supporting
> > Windows for xia2 / DIALS - however there are a bunch of rather
> > nasty jobs to do in making this possible and it’s never “the most
> > important thing” sorry :-(
> >
> > Happy new year & best wishes Graeme
> >
> > On 22 Dec 2020, at 16:53, Irwin Selvam <  
> > irwin.sel...@postgrad.manchester.ac.uk> wrote:  
> >
> > Hi,
> >
> > I'd like to reprocess some data that were collected on an Eiger2
> > detector at Diamond with Xia2Dials using CCP4i2's GUI. I'm running
> > CCP4i2 on a 64-bit Windows 10 machine. The data were processed
> > successfully at Diamond with no obvious pathologies, the high
> > resolution limit was just a little generous. The folder in question
> > contains a Diamond specific file (.nsx extension), two image files
> > (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've
> > tried pointing Xia2 to the folder itself (which works when
> > processing data collected on PILATUS detectors) and each of the
> > files contained therein (except the Diamond specific file). Each
> > time this results in the error " -ERROR- None:56 Error in wrapper
> > xia2_dials 0.0:: External process exited with exit code != 0
> > Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in
> > wrapper xia2_dials 0.0:: Error in checking external process after
> > completion exit status and code: 0 1". I've attached the error,
> > debug etc files for a representative 'run' to this email. Which
> > files do I need to point xia2 towards to get it to run? Any help
> > would be appreciated.
> >
> > All the best,
> >
> > Irwin
> >
> > --
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> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > 
> >
> >
> >
> >
> > --
> >
> > This e-mail and any attachments may contain confidential, copyright
> > and or privileged material, and are for the use of the intended
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> > Any opinions expressed within this e-mail are those of the
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> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> > attachments are free from viruses and we cannot accept liability
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> > viruses which may be transmitted in or with the message.
> > Di

Re: [ccp4bb] version for old AMD processors

2020-12-10 Thread Tim Gruene
Dear Gottfried,

you can compile from source, http://www.ccp4.ac.uk/download/#os=src 

and/or spend 150-200Euro for a new computer.

Best,
Tim

On Thu, 10 Dec 2020 12:07:17 +0100
"Palm, Gottfried"  wrote:

> Dear all, 
> 
>   I am running into a "known issue" upon installing ccp4-7.1 on a
> pre2010 AMD machine. The download page says
> 
> 
> 
> CCP4 7.1: Known issues
> ...
> Old AMD processors
> ...
> We are in the process of preparing an alternative release package for
> those processors. 
> 
> 
> 
> Is there a solution in the meanwhile?
> Greetings
>   Gottfried
> 
> 
> 
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Re: [ccp4bb] wsl2 Ubuntu 20.04

2020-12-07 Thread Tim Gruene
Dear Johannes,

w.r.t. shelx-binaries:

you can check with 
#> cat /proc/cmdline
whether the linux-kernel option include 'vsyscall=emulate'.

Quite some time ago, the linux kernel made vsyscall obsolete. The
SHELX-binaries are probably compiled with an old compiler on an
old linux system, and require this kernel option to run.
Otherwise they trigger a segmentation fault.

vsyscall's are considered a small security hole, but unless you run a
safety-critical machine, you can probably risk to open this hole in
your kernel at the benefit of running the SHELX programs.

This link might be related:
https://github.com/microsoft/WSL/issues/4694

Cheers,
Tim


On Mon, 7 Dec 2020 13:50:23 +0100
Johannes Cramer  wrote:

> Dear board,
> 
> has anyone gotten ccp4 (specifically shelx and arpwarp) installed and
> working under wsl2 (windows subsystem for linux)?
> arp warp refuses to install with the following error:
> 
> Segmentation fault
> *** ERROR ***
> This machine cannot run ARP/wARP executables that
> are statically linked to glibc.
> 
> shelx does not complain during installation, but when I type shelxc
> (or shelxd, shelxe, shelxl, shelxt)  I get immediately to the promt.
> No error message or anything.
> I am using Ubuntu 20.04 LTS.
> 
> Any help would be appreciated.
> 
> Cheers,
> Johannes
> 
> 
> 
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[ccp4bb] Workshop on electron crystallography Dec 17th 2020

2020-12-04 Thread Tim Gruene
Dear all,

on behalf of the organisers, I would like to draw your attention to a
workshop on electron crystallography, taking place December 17th
2020. Its purpose is to update of developers and users in the field
with the current state of their research.

You find more information and a link to the registration at the
workshop URL
https://www.uni-ulm.de/en/einrichtungen/hrem/christmas-elec-crystall/christmas-elec-crystall/

The workshop program will soon be available.

Best regards,

TG on behalf of Tatiana Gorelik, Mauro Gemmi, Lukas Palatinus, and
Stephanie Kodjikian

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Re: [ccp4bb] Stabilizing Mitegen reusable bases/mounts

2020-11-15 Thread Tim Gruene
Dear Patrick,

you can use ordinary glue ("Uhu Sekundenkleber") or nail varnish to glue
the pin into the base. To remove the pin, just keep it in a beaker with
acetone. Both glue and varnish resolve within short time (an hourish?)
This has been practice in the labs where I worked for the past 20
years. I am surprise Mitegen found a market for their 'resuable' bases.

Best,
Tim

On Sun, 15 Nov 2020 15:45:01 -0500
Patrick Loll  wrote:

> Hi everyone,
> 
> I’ve become very fond of the Mitegen reusable bases for mounting
> crystals, since the reusable aspect savse me from having to discard
> the base every time I break a microloop. However, once the crystals
> arrive at the synchroteon, I observe motions of the loops (some
> gradual, some sporadic). The the amplitudes of these motions are
> becoming significant as I take data from smaller and smaller
> crystals. I don’t think I’m imagining this, since the good folks at
> NSLS-2/AMX have warned me about this very issue.
> 
> I’m writing to ask if anyone has any clever ideas about stabilizing
> these assemblies. Obviously, I can epoxy the pins in place, but then
> I’ll probably need to discard the entire assembly when I break a
> loop, and I’d prefer not to waste more money than necessary. I’ve
> considered putting a bead of wax at the point where the pin enters
> the base (although I haven’t yet checked to see if that will survive
> immersion in liquid nitrogen). Does anyone have any other (better)
> ideas?
> 
> Much obliged in advance,
> 
> Pat
> __
> 
> Patrick J.  Loll, PhD
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St.
> Philadelphia, PA 19102-1192 USA
> 
> (215) 762-7706
> pj...@drexel.edu
> 
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Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

2020-11-12 Thread Tim Gruene
as
> > rigorous as possible:
> >
> > - is there a 'best practices' order of refinement operations?
> > e.g. refine the lattice parameters first, then peak profiles, etc.
> > - there is a single peak that is not matching (likely due to a
> > slight deviation in atomic positions from the expected simple
> > cubic structure) - is refinement capable of moving individual
> > atoms or clusters of atoms to better match a small, unaccounted
> > for reflection?
> >
> > For what it's worth, I have been using Reflex in Materials
> > Studio; if there is a more appropriate software for this
> > application, I would be happy to hear!
> >
> > If any additional clarification is need, I'll fill it in!
> >
> > Best,
> > Kamil
> >
> > 
> >
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Re: [ccp4bb] R free rising

2020-11-04 Thread Tim Gruene
Dear Nika,

XDS probably did what you asked it to do ;-)

This is, however, not a problem. You only need to refine for a couple
of rounds longer to gain independence of your Rfree set. No need to
reassign them. Depending on the refinement program, it may take many
rounds. With Refmac (or shelxl), it does not take very long.

Wenn you plot the LLgain, listed at the end of the refmac log-file, and
its curve flattens out, your Rfree reflections should be independent
and not model-biased anymore.

Best regards,
Tim

On Wed, 4 Nov 2020 13:18:06 +
Nika Žibrat  wrote:

> Hello,
> 
> Two days ago I was asking about R free rising. The problem was xds
> adds R free flags already and then re-introduced them in Phenix,
> causing R free to rise. I would like to thank you for your answers,
> they were most helpful.
> 
> Best,
> Nika
> 
> 
> From: Nika Žibrat
> Sent: ponedeljek, 02. november 2020 11:26
> To: ccp4bb@jiscmail.ac.uk
> Subject: R free rising
> 
> 
> Hello,
> 
> 
> 
> I am trying to solve an X-ray structure of a protein of which the
> structure is already known. My aim is to only seek for ligands
> (soaking) and interpret any conformational changes. Since I am using
> a model with 100% sequence identity from PDB I am not doing Autobuild
> after Molecular phasing and continue directly with phenix.refine
> according to reccomendations (10 rounds). In accordance with X-triage
> I am also using NCS default settings in the refinement.
> 
> 
> 
> This refinement produces solid R free and R work values around 0.29
> and 0.22. The problem becomes when I want to manually edit the
> structure, correct the loops which are changed upon binding of the
> ligand, and correct any outliers. This results in R free slightly
> lower than R work. Upon refining, R work drops normally while R free
> rises significantly (for 0.2 -0.3). I have been trying to crack this
> for a few days with no success.
> 
> 
> 
> I read that slightly lower R free can be normal in such cases but
> nevertheless both R values should drop, and haven't found anything
> about the big rise of this value after refinement. It feels like I am
> missing something, since this is my first time solving a structure.
> Any advice?
> 
> 
> 
> Thank you,
> 
> Nika
> 
> 
> 
> 
> 
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Re: [ccp4bb] [xds] how to specify measuring angle

2020-10-08 Thread Tim Gruene
Dear Doo Nam Kim,

the indexing procedure is independent of the starting angle of the
first frame.

Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree
per frame during data collection?

Best regards,
Tim

On Thu, 8 Oct 2020 09:28:07 +0100
Doo Nam Kim <4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote:

> I think that my microED data was measured with -60 to 60 rotation
> angle.
> 
> However, 
> STARTING_ANGLE=  -60.
> in my XDS.INP
> 
> resulted in 
> ...
>   #  COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES
> 
> 1   0.0020349 0.0108237 0.0096964 1.00   -0.00   -0.00
> 2  -0.0056895-0.0002762 0.0015024 0.001.00   -0.00
> 3   0.0011313-0.0034716 0.0036457 0.00   -0.001.00
> 
> 
>  * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1
> * !!! ERROR IN REFINE !!! RETURN CODE IS IER=   0
> 
> I assume that rotation angle should be specified in XDS.INP.
> 
> Anyone knows how to specify measuring angle in XDS.INP?
> 
> If there's no such option in XDS.INP, please let me know as well.
> Then, my other part of XDS.INP should be corrected.
> 
> Thank you
> 
> 
> 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-09 Thread Tim Gruene
Hi Eike,

one of the points is that, only because you got used to a certain
operation (over many years after someone showed it to you), does not
mean it is intuitive. This could be judged by e.g. showing an ignorant
user both methods and let the person judge which one is easier to use...

Cheers,
Tim

On Wed, 9 Sep 2020 20:27:55
+ "Schulz, Eike-Christian"  wrote:

> Hi Tim, 
> 
> I don't think that metaphor is quite correct. To me it seems that no
> matter what button you pushed you got coffee. In my opinion intuitive
> software is a blessing and should not easily be disregarded. 
> 
> But as I said before, I am happy to read into new stuff. 
> 
> Also there seem to be mixed experiences here. Might this be
> map-resolution related ? 
> 
> Best, 
> 
> Eike
> 
> 
> 
> -Original Message-
> From: CCP4 bulletin board  on behalf of Georg
> Zocher  Reply to: Georg Zocher 
> Date: Wednesday, 9. September 2020 at 22:17
> To: "CCP4BB@JISCMAIL.AC.UK" 
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot
> 0.8
> 
> Dear Herman,
> 
> Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
> > The old real-space refinement was intuitive and easy to use and
> > did exactly what the user expected, without having to consult
> > the manual! The result might not have been perfect, but was
> > good enough for subsequent Refmac, Buster, Phenix refinement.  
> 
> That fits perfectly to my user experience with RSR in coot 0.8.x.
> and also explains why at least a number of people having some issues
> with the new RSR.
> 
> All the best,
> 
> Georg
> 
> 
> 
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> 
> 
> 
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Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-09 Thread Tim Gruene
Dear Georg and others, 

if I followed the thread correctly, the coffee story should really go
like this:

for years you have been pushing the button of a machine
showing a cup with a black liquid inside. After ten years, the
manufacturer of the machine tells you:
"Sorry guy, it is not coffee what you have been drinking. If
you want to drink coffee, you should push the button down here, which
is labelled 'coffee'."
Because you drank the other liquid for years, you are very
disappointed by the taste of real coffee and keep on pushing the old
button that you got used to.

That's how I interpret Paul's statement 
"[...] many people learnt (I discovered, rather late in the day) [...]"

Has anyone of the disappointed users asked how to do it properly? Maybe
it is just as easy.

Cheers,
Tim

On Wed, 9 Sep 2020 17:22:27 +0200
Georg Zocher  wrote:

> Dear Paul,
> 
> people are complaining that they have issues fitting their model in
> real space using coot 0.9.x. Personally, I very briefly used coot
> other the last months but also have problems using RSR properly
> because I'm used to do it the way it was over the last 10 years. This
> might be due to my ignorance that I did not have a more closer look
> into the new features of RSR in 0.9 release and how to use them. But
> from the user site it's different to handle now.
> 
> I do not understand your Ferrari comparison (sorry) as I would not
> buy one even if I would have more money than one can spend. But I
> would take a cup of coffee as an example. If you always go to the
> same dealer to get your coffee in the morning as you know you get a
> very descent and excellent tasting cup of coffee that you fully enjoy
> every morning than you really get used to it. It might be than a hard
> time for you if your coffee dealer tells you: Sorry guys, I do have
> now an optimized coffee that is much better, taste a lot better, is
> fair produced,... It's just not the coffee you drunk over the last 10
> years and I will not offer that one anymore. You might give the new
> one a chance, you might find it as excellent as the dealer but you
> might not. From my point of view it's the lack of choice that
> personally I do not like so much, especially if there is no other
> coffee dealer around...
> 
> Nevertheless, I'm aware and fully respect all the effort you put in
> the development of coot and I'm really grateful that coot is
> available.
> 
> All the best,
> Georg
> 
> 
> 
> Am 08.09.20 um 17:44 schrieb Paul Emsley:
> > On 08/09/2020 16:25, Georg Zocher wrote:  
> >>
> >>
> >> we have the same experience in our lab.  
> >
> >
> > What experience is that? I am still in the dark about you think is
> > now worse.
> >
> >  
> >> Personally, I did would not like to judge here, as so far, I did
> >> not have had enough time to get into the new RSR of coot 0.9.x by
> >> myself. But many colleagues did not like the new refinement module
> >> maybe just as they are used to the method in all coot versions
> >> before.  
> >
> >
> > You have a Ferrari parked beside your house but you want to to take 
> > the bus to work because that's what you've always done. Or maybe
> > the Ferrari is parked around the back and you don't know it's there?
> >
> >  
> >>
> >> I just thought if it wouldn't be an option to let the user decide 
> >> what kind of RSR implementation she/he would like to use and give 
> >> them the choice via an option in coot preferences?  
> >
> >
> > That would be possible but not easy. Unlike much of the CCP4 suite, 
> > Coot is Free Software. But, again... why would you want to take the 
> > bus? Explain.
> >
> >
> > regards,
> >
> >
> > Paul.
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
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> 
> 
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Re: [ccp4bb] Omega angles with molprobity

2020-09-04 Thread Tim Gruene
Hi Joana,

unless you are constrained to a molprobity tool, you could use the CCP4
program ANGLES to list the omega angle for each residue. See
$CEXAM/unix/runnable/angles.exam
for an example.

Best,
Tim


On Fri, 4 Sep 2020 11:28:47 +0200
Joana Pereira  wrote:

> Dear all,
> 
> Does anyone know which molprobity tool in ccp4/bin lists the omega 
> angles for each residue? I see Phenix provides a comprehensive 
> validation based on Molprobity and, from what I understand, lists the 
> omega angles for each residue. However, I am having troubles to find 
> which molprobity tool provides that info. Any idea?
> 
> Many thanks!
> 
> Best wishes
> 
> Joana Pereira
> 



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Re: [ccp4bb] diffdump in CCP4 7.1

2020-08-21 Thread Tim Gruene
Dear David,

Kay Diederich's generate_XDS.INP
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
creates the full XDS.INP for you for a large number of frame formats.
It is not CCP4, but I think there are no restrictions for using it.

Best regards,
Tim

On Fri, 21 Aug 2020 14:29:26 -0700
Jan Abendroth  wrote:

> Hi all,
> 
> It looks as if the utility ‘diffdump’ is no longer part of the
> standard linux CCP4 7.1 distribution.
> 
> It has been a very handy tool for preparing XDS input files.
> 
> Does anyone know if there is an equivalent script in CCP4 7.1?
> 
> 
> 
> Thanks,
> 
> Jan
> 




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Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-30 Thread Tim Gruene
0.0848  |--|  0.5017  |  0.4906  |
> |  9   | C 2 2 21   |  0.0871  |--|  0.5059  |  0.4928  |
> | 10   | P 43 21 2  |  0.0919  |--|  0.5180  |  0.5109  |
> -
> | <<  10   | P 43 21 2  |  0.0919  |--|  0.5180  |  0.5109  |
> -
> 
> R-factor in the original subgroup is (almost) the best.
> The original spacegroup assignment seems to be correct.
> 
> According the non-crystallography translation vector, there is an
> output from xtriage:
> 
>-
>| XYZ  | height   | p-value(height) |
>-
>|  0.000, 0.000, 0.334 |   53.049 | 4.456e-05   |
>|  0.000, 0.000, 0.167 |   28.966 | 1.681e-03   |
>|  0.000, 0.000, 0.500 |   27.692 | 2.102e-03   |
>-
> 
> 
> Jon Cooper wrote:
> > Hello, have you tried anisotropic B-factor refinement? It is
> > usually very good at cleaning-up the difference map. At that sort
> > of resolution, you may still have some way to go in the refinement
> > since the R and R-free usually go to about half of what you have,
> > at least with proteins.  
> 
> Dear Jon. Yes, I used anisotropic refinement as usually for this sort
> of resolution (1.4 A or better). But it looks too high for this small 
> object and very high resolution, in my opinion.
> 
> Best regards,
> 
> Rafal
> 
> 
> 
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Re: [ccp4bb] [EXTERNAL] chirality with electron diffraction

2020-07-20 Thread Tim Gruene
Dear Herman,

no, I don't think this is routine, yet! 
First of all, instrument manufacturers need to catch up. What's on the
market is quite behind what is possible - although, I don't have the
instrument I'd love to have, but at least the meta data transfer to the
image headers only works when you work with a native CCD camera (stone
age, I know), not with a hybrid pixel detector.

Secondly, Lukas Palatinus' software is, as far as I know, not yet
compatible with the rotation method, i.e. when you use XDS or DIALS or
mosflm, etc, you cannot use his software for dynamic refinement. I also
understand that dynamic refinement is quite time consuming. Lukas is
working on this, though.

Best wishes,
Tim

On Mon, 20 Jul 2020 10:36:49 +
"Schreuder, Herman /DE"  wrote:

> Hi Tim,
> 
> thank you for your reply. The 1998 Schenk paper is "new" to me, I had
> seen this one:
> https://science.sciencemag.org/content/sci/364/6441/667.full.pdf The
> background of my question was about the status in practice: Is it
> possible to routinely determine the absolute configuration of small
> molecules by electron diffraction, or is it something that in theory
> can be done, but only difficult in practice?
> 
> Best,
> Herman
> 
> 
> 
> -Ursprüngliche Nachricht-
> Von: Tim Gruene  
> Gesendet: Montag, 20. Juli 2020 11:03
> An: CCP4 bulletin board ; Schreuder, Herman
> /DE  Betreff: [EXTERNAL] chirality with
> electron diffraction
> 
> EXTERNAL : Real sender is  tim.gru...@univie.ac.at   
> 
> 
> 
> Dear Herman,
> 
> The absolute configuration can be determined, although very
> differently from X-ray ccrystallography.
> 
> So far, two different experimental approaches have been published: 
> Ma, Oleynikov, Terasaki (2017), https://doi.org/10.1038/nmat4890
> 
> and Brazda et al (2019), 10.1126/science.aaw2560 
> 
> The former is based on imaging, the latter is based on dynamical
> refinement: Jansen, Tang, Zandbergen, Schenk (1998),
> https://doi.org/10.1107/S0108767397010489
> 
> There is a very interesting paper by Burmester and  Schroeder
> Scanning Microscopy Vol. 11, 1997 (Pages 323-334). According to this
> paper, the anomalous signal in ED is actually stronger than in X-ray
> crystallography. As far as I know, this has not been pursued further.
> 
> Best wishes,
> Tim
> 
> P.S.: This is a response to your email to Jessica Bruhns in the
> thread 'quote source inquiry'. This thread has reached an overflow,
> so I took the liberty to adjust the subject.
> 
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis Faculty of Chemistry
> University of Vienna
> 
> Phone: +43-1-4277-70202
> 
> GPG Key ID = A46BEE1A



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[ccp4bb] chirality with electron diffraction

2020-07-20 Thread Tim Gruene
Dear Herman,

The absolute configuration can be determined, although very differently
from X-ray ccrystallography.

So far, two different experimental approaches have been published: 
Ma, Oleynikov, Terasaki (2017), https://doi.org/10.1038/nmat4890

and Brazda et al (2019), 10.1126/science.aaw2560 

The former is based on imaging, the latter is based on dynamical
refinement: Jansen, Tang, Zandbergen, Schenk (1998),
https://doi.org/10.1107/S0108767397010489

There is a very interesting paper by Burmester and  Schroeder
Scanning Microscopy Vol. 11, 1997 (Pages 323-334). According to this
paper, the anomalous signal in ED is actually stronger than in X-ray
crystallography. As far as I know, this has not been pursued further.

Best wishes,
Tim

P.S.: This is a response to your email to Jessica Bruhns in the thread
'quote source inquiry'. This thread has reached an overflow, so I took
the liberty to adjust the subject.

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Faculty of Chemistry
University of Vienna

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Re: [ccp4bb] Quote source inquiry

2020-07-17 Thread Tim Gruene
Dear Garib,

thank you very much for the details! If everything goes to plan, we are
going to use the Dectris QUADRO in September(ish), ideally also with
some protein crystals. In ED, distance calibration is more difficult
than with X-rays because of instabilities in the lens system (at least
with the older instruments), and because I do not work with a parallel
beam, but focus the beam onto the detector surface. This is not a very
reproducible process. In those cases where I got high resolution data,
the cell is often quite stable, and the distance can vary by about 5%...

Best regards,
Tim

On Thu, 16 Jul 2020 23:21:54 +0100
Garib Murshudov  wrote:

> One correction: Model should after molecular replacement and few
> cycles of refinement (perhaps with a little bir relaxed geometry, but
> not too much).
> 
> There is an option to use a model after molecular replacement but it
> is being migrated to another program that will have proper tests.
> 
> Regards
> Garib
> 
> 
> > On 16 Jul 2020, at 22:34, Garib Murshudov 
> > wrote:
> > 
> > Hi Tim,
> > 
> > There is an option to do unit cell parameter refinement (for all
> > six parameters in general which can only happen in P1). It is
> > undocumented. 
> > 
> > Celrefine/lattice refine all # if you give scale instead of all
> > then only one parameter is refined.
> > 
> > Cellrefine select .  # use only atomic B value < Bmedian +
> > alpha * Binterquartile_range
> > 
> > 
> > The last command was added to to reduce effect of wrong atoms.
> > 
> > These command should enable refinement all parameters with due
> > account for symmetry. But I am worried about refinement of cell
> > parameters using atomic models. The problem is that it affects B
> > values and I think if model is not good then cells will be expanded
> > to reduce non-bonding interactions. I think it will give biased
> > results. For ideal case (when you deliberately change cell
> > parameters) it worked perfectly when I tried. However, for real
> > cases I could not convince myself to claim that it would give
> > unbiased results. My current thought is that either a model after
> > molecular replacement should be used or cell parameters should be
> > refined outside using data only (then you can only make cell
> > parameters consistent with each other). 
> > 
> > If you still would want to use refmac to do this calculations then
> > you should do it iteratively. Refine cell, then change mtz file
> > (different cell parameters) then refine cell again. Please also
> > note that if you are refining cell parameters then the resolution
> > of the data will also change (if you are refining all six
> > parameters then changes will be anisotropic)
> > 
> > 
> > In general it is a trivial but extremely trivial problem.
> > 
> > Regards
> > Garib
> > 
> > 
> >   
> >> On 16 Jul 2020, at 18:31, Tim Gruene  >> <mailto:tim.gru...@univie.ac.at>> wrote:
> >> 
> >> Hi Jessica,
> >> 
> >> Jens Luebben wrote cellopt for this purpose. It is available from
> >> github, https://github.com/JLuebben/CellOpt
> >> <https://github.com/JLuebben/CellOpt>
> >> 
> >> It is based on the idea available in whatcheck, i.e. to optimise
> >> the unit cell parameters based on geometry restraints DFIX/DANG.
> >> Those need to be three-dimensional: I've had cases where the
> >> restraints do not span all three dimensions. In this case one of
> >> the cell parameters can refine to unrealistic values. 
> >> 
> >> We are quite slow on the manuscript for its reference, but for the
> >> time being, please quote the nanoArgovia (www.nanoscience.ch
> >> <http://www.nanoscience.ch/>) project A12.01 (A3EDPI).
> >> 
> >> cellopt is called liked a shelxl job, i.e. like 'cellopt name'
> >> where name.ins and name.hkl are present in the directory. You can
> >> add some constraints to the lattice type. 
> >> 
> >> Refmac5 can also refine the unit cell parameters (Max Clabbers has
> >> made use of this feature), but as far as I understand, refmac5
> >> only scales the unit cell volume isotropically - I am happy to be
> >> corrected.
> >> 
> >> When you resolution is quite high, say 0.7A like what we get for
> >> zeolites and some organic compounds, you can refine the cell and
> >> the distance simultaneously, only the BEAM correlates heavily with
> >> the distance. DIALS can produce plots for the correlation between
> >> refined 

Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread Tim Gruene
. Kleywegt
> > >
> > >  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> > > **
> > >   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 !
> > > **
> > >
> > > ##
> > > ##
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
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> >
> > 
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> 
> 



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Re: [ccp4bb] Accessing full list of programs in CCP4I2

2020-07-07 Thread Tim Gruene
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Re: [ccp4bb] Lost extension bar in Coot

2020-06-11 Thread Tim Gruene
Dear Kahkashan,

check out the Calculate->Modules... menu.

Best,
Tim

On Thu, 11 Jun 2020 17:56:11 +0530
Firdous Tarique  wrote:

> Hi
> 
> Just downloaded the new CCP4-7.1. Wondering where the extension bar
> in Coot 0.9 has gone. Please help me to find it. I think it is hidden
> somewhere.
> 
> Best
> 
> Kahkashan
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Question about small molecule crystallography

2020-06-02 Thread Tim Gruene
Dear Francois,

provided you are not restricted to the trademark term 'microED', but
open minded to include '3D electron crystallography', there are plenty
of published structures of small compounds, both organic and inorganic.
Several of them date back to 2005, and include complex structures
like MOFs, (Xiaodong Zou, Stockholm), twinned structures
(Gemmi/Mugnaioli, Pisa), and really good quality work (Parsons/Zou).

Usually, crystals are not "present in powder", they compose the powder,
in particular if you use products at 99.9% purity from Sigma-Aldrich
'off the shelf' is it was put, and such powders are not
amorphous (if you read bioarxiv) or 'simingly amorphous' (if you read
the peer-reviewed version)...

Scotch is not the same as adhesive tape, and pampers is not the same as
diapers (c.f. also Gerard Bricogne's post on this bb, 29th April 2020).

Best,
Tim



 On Tue, 2 Jun 2020 10:52:45 +0200
hoh  wrote:

> Hi everyone
> 
> 
> Pr Tamir gonen (UCLA, los Angeles) have solved (not published) few 
> chemical compounds structures with mircoED. And, the more important
> is that crystals were present in the powder (whatever condtions to
> get it (preciptation, evaporation ..). I have myself test with 2
> powders coming from Chemists, here in Montpellier, and there were
> bunch of nano crystals in both powders, and both diffract at 0.6 A.
> And, as the wavelenght in microED in very short  , Xds or Dials (with
> some specifics parameters) are working well. And ,finally, you need
> only  around 0.01ug of product to put on the grid (without blotting,
> in dry method) with result almost warranty
> 
> So, think about microED for small molecules..
> 
> FH
> 
> 
> François Hoh
> 
> Centre de Biochimie Structurale,
> UMR 5048 CNRS, UMR 1054 INSERM
> 29, rue de navacelles
> 34090 Montpellier Cedex, France.
> Phone: +33 467 417 706
> Fax:   +33 467 417 913
> 
> 
> 



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--
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Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-28 Thread Tim Gruene
Dear Eddie, dear all

According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article
appeare in Newsletter June 95. It is mentioned in the table of contents,
"Correction on perfection: primary extinction correction in protein
crystallography" by Polykarpov and Sawyer.
Unfortunately, the article itself is not there

Extinction is not the same as the dynamic effects that James mentioned,
but this seems the closest match.

Would anyone have a copy they can share with me?

Thanks a lot!

Best,

Tim 

On Thu, 28 May 2020 15:43:00 +
Edward Snell  wrote:

> This jogged my memory of a CCP4 newsletter article many years ago
> covering kinematical versus dynamic scattering in protein crystals
> and offering a correction that could be used. I think it was Lindsay
> Sawyer and Igor Polikarpov in the late 90’s. I apologize if I have
> the authors wrong but I thought it was a commentary well ahead of its
> time and with modern sources and low noise detectors, I am wondering
> if anyone has revisited this? Protein crystals are remarkably high
> quality until you cryocool them. Serial methods combined with
> instrument capabilities may rate a revisit to the use of the
> kinematical approximation versus application of dynamical theories?
> Certainly the computational power is available.
> 
> Just my 2 cents for the day.
> 
> Best,
> 
> Eddie
> 
> 
> Edward Snell Ph.D.
> 
> Director of the NSF BioXFEL Science and Technology Center
> President and CEO Hauptman-Woodward Medical Research Institute
> BioInnovations Chaired Professorship, University at Buffalo, SUNY
> 700 Ellicott Street, Buffalo, NY 14203-1102
> hwi.buffalo.edu<http://hwi.buffalo.edu/>
> Phone:   (716) 898 8631 Fax: (716) 898 8660
> Skype:eddie.snell Email:
> esn...@hwi.buffalo.edu<mailto:esn...@hwi.buffalo.edu> Webpage:
> https://hwi.buffalo.edu/scientist-directory/snell/ [hwilogo]
> Heisenberg was probably here!
> 
> 
> 
> From: CCP4 bulletin board  On Behalf Of James
> Holton Sent: Thursday, May 28, 2020 11:34 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Strange Pseudosymmetry Effects
> 
> Be careful with electron diffraction and apparent absence violations.
> It is possible these weak spots are simply due to multiple
> scattering.  If so, you would see them relatively stronger with
> larger crystals,but much weaker relative to the strong reflections
> when the crystal is smaller. Do you?
> 
> -James Holton
> MAD Scientist
> On 5/27/2020 6:49 PM, Jessica Bruhn wrote:
> Hello,
> 
> I am wondering if pseudosymmetry can cause weak reflections that
> mimic the doubling of one unit cell axis' length. Has anyone seen
> something like this before?
> 
>  I am processing data from a small molecule sample collected with
> electron diffraction from multiple crystals. For the b axis, it is
> not clear if the length should be 10A or 20A. There are spots with
> the correct spacing for b=20A, but every other spot seems weaker than
> the spots along k if I choose b=10A (this extends beyond (0,k,0)). I
> am unable to phase the b=20 data. I have solved this structure in P1
> with b=10 and found four molecules in the ASU and in P212121 with
> b=10 resulting in one molecule in the ASU. In P1, three of the four
> molecules adopt the same conformation, but the fourth molecule is in
> an alternate conformation that causes only ~1/2 of the molecule to be
> consistent with the first three. In P212121 I see density for part of
> this alternative conformation, but the full molecule in this
> alternate conformation cannot pack properly in P212121. Based on
> these results and some orthogonal data, I think I should refine the
> solution in P1 with b=10. Does it seem reasonable that pseudosymmetry
> is causing these weak reflections along k hinting at a doubling of
> the b axis?
> 
> Thanks in advance!
> 
> Best,
> Jessica
> 
> --
> Jessica Bruhn, Ph.D
> Principal Scientist
> NanoImaging Services, Inc.
> 4940 Carroll Canyon Road, Suite 115
> San Diego, CA 92121
> Phone #: (888) 675-8261
> www.nanoimagingservices.com<http://www.nanoimagingservices.com>
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> 
> 
> 
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> 
> 
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> 
> Thi

Re: [ccp4bb] What refinement programs are fully Open Source?

2020-05-07 Thread Tim Gruene
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1data=02%7C01%7Cpr159%40leicester.ac.uk%7Cf8cc2fb23bb84707d7a708d7f2a96338%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637244681673138009sdata=nfhtEWy2FS96MYwaHsT4qoQi%2BMbPetQdTwfAf3FDjGg%3Dreserved=0
> >  
> 
> 
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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--
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University of Vienna

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Re: [ccp4bb] disinfecting keyboards

2020-05-06 Thread Tim Gruene
> >> *To:* CCP4BB@JISCMAIL.AC.UK
> >> *Subject:* Re: [ccp4bb] disinfecting keyboards
> >>
> >> EXTERNAL MAIL
> >>
> >> ​You could try doing what my technician does with her keyboard;
> >> she wraps it in a clear, thin food wrap that can be taped to the
> >> back of the keyboard. This is usually done to keep food and other
> >> things (liquids) from damaging the keyboard, but you could simply
> >> replace the wrap every time someone else uses it.
> >>
> >>
> >> Personally I like using a Kimwipe soaked with 100% isopropanol,
> >> I've never yet encountered a keyboard that suffered from having
> >> the writing removed with that or 100% ethanol. Both work and as
> >> long as they are 100% (no water), the keyboard and mouse have no
> >> issues.
> >>
> >>
> >> Diana
> >>
> >>
> >> **
> >> Diana R. Tomchick
> >> Professor
> >> Departments of Biophysics and Biochemistry
> >> UT Southwestern Medical Center
> >> 5323 Harry Hines Blvd.
> >> Rm. ND10.214A
> >> Dallas, TX 75390-8816
> >> diana.tomch...@utsouthwestern.edu
> >> (214) 645-6383 (phone)
> >> (214) 645-6353 (fax)
> >> 
> >> *From:* CCP4 bulletin board  on behalf of
> >> Tim Gruene 
> >> *Sent:* Wednesday, April 29, 2020 1:53 PM
> >> *To:* CCP4BB@JISCMAIL.AC.UK
> >> *Subject:* [ccp4bb] disinfecting keyboards
> >> Dear all,
> >>
> >> can you make suggestions for how to disinfect computer keyboards,
> >> and instrument panels?
> >>
> >> Our facility is going to reboot next week, with shifts so that
> >> people don't meet. The main interface will be the computer
> >> keyboards, as well as the door of our X-ray diffractometer and the
> >> mounting of the crystals.
> >>
> >> The keyboard labels may not like alcohols (and the efficiency of
> >> injecting disinfecting through the USB cable is also under
> >> discussion, so I heard).
> >>
> >> One way would be to use individual keyboards, and wearing gloves
> >> for replugging, and to use gloves for mounting crystals.
> >>
> >> But maybe there are other ways that won't require gloves?
> >>
> >> Best regards,
> >> Tim
> >>
> >> -- 
> >> --
> >> Tim Gruene
> >> Head of the Centre for X-ray Structure Analysis
> >> Faculty of Chemistry
> >> University of Vienna
> >>
> >> Phone: +43-1-4277-70202
> >>
> >> GPG Key ID = A46BEE1A
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >>
> >> 
> >>
> >> UTSouthwestern
> >>
> >> Medical Center
> >>
> >>
> >> The future of medicine, today.
> >>
> >>
> >> ------------
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >>
> >> CAUTION: This email originated from outside UTSW. Please be
> >> cautious of links or attachments, and validate the sender's email
> >> address before replying.
> >>
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >>  
> > --
> > Dr. Andrea Thorn | group leader
> > andrea.th...@uni-wuerzburg.de
> > +49 931 31-83677
> >
> > Rudolf Virchow Center, University of Wuerzburg
> > Josef-Schneider-Str. 2 | 97080 Wuerzburg | Germany
> > https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >  
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



-- 
--
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Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] disinfecting keyboards

2020-04-29 Thread Tim Gruene
Dear all,

can you make suggestions for how to disinfect computer keyboards, and
instrument panels?

Our facility is going to reboot next week, with shifts so that people
don't meet. The main interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Tim Gruene
Hallo Fred,

lsqman (Uppsala software factory) is another option. With lsqman you
can give explicit atom names, so that it works e.g. even for small
molecule structures that do not follow PDB conventions.

@Paul Emsley: a graphical option that let's you e.g. click on 2x3
corresponding atoms in Coot would come very handy ;-)

Best,
Tim

On Fri, 24 Apr 2020 13:08:26 +0200
"Fred. Vellieux"  wrote:

> Hi folks,
> 
> Some of you may have had to do this already. Either in the lab or
> more recently perhaps from home.
> 
> I have two structures that I wish to superpose (two protein:dsDNA 
> complexes). Not using the protein part, but superposition through the 
> dsDNA.
> 
> I'm not quite certain what is the "best" way of doing this.
> 
> Your suggestions will be appreciated, thanks.
> 
> Fred. Vellieux
> 



-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] New phasing approach

2020-04-01 Thread Tim Gruene
Dear Bernhard,

your paper is actually not so much of a joke. Are you aware of K. Huemmer's 
and E. Weckert's three-beam experiments? See e.g. 

https://link.springer.com/chapter/10.1007/978-1-4615-5879-8_24

Best regards,
Tim

On Wednesday, April 1, 2020 4:00:19 AM CEST Bernhard Rupp wrote:
> Hi Fellows,
> 
> 
> 
> just in time for a little reading during quarantine-induced boredom here
> preprint pages
> 
> (embargoed until 04.01) from my recent Phys. Rev. paper with a different
> take on phasing
> 
> https://tinyurl.com/Phys-Rev-2020
> 
> 
> 
> Enjoy, BR
> 
> --
> 
> Bernhard Rupp
> 
>  <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/
> 
>  <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org
> 
> +1 925 209 7429
> 
> --
> 
> Department of Genetic Epidemiology
> 
> Medical University Innsbruck
> 
> Schöpfstr. 41
> 
> A 6020 Innsbruck
> 
>  <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at
> 
> +43 676 571 0536
> 
> --
> 
> Many plausible ideas vanish
> 
> at the presence of thought
> 
> --
> 
> 
> 
> 
> ########
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight

2020-04-01 Thread Tim Gruene
Dear Jurgen,

https://lmgtfy.com/?q=ccp4+twitter

do you need more?

Best,
Tim

On Wednesday, April 1, 2020 5:19:13 PM CEST Jurgen Bosch wrote:
> #theBB is too slow :-), Honestly, we probably should have an official CCP4BB
> Twitter account monitored by a few administrators to post relevant things
> more publicly - just a thought.
> 
> Thanks for the update and good to know it’s moving forward fast.
> I had to renew my license for a software I use for shape complementarity
> searches, so I have not been able yet to contribute, but I reached out to
> my MedChem friends and made them aware of it. Even if they can’t synthesize
> stuff right now because we are mostly shut down, they can use their brains
> to make suggestions.
> 
> Jürgen
> 
> > On Apr 1, 2020, at 10:15 AM, Frank von Delft 
> > wrote:
> > 
> > All - last week's call for compound designs to the CoV-2 main protease
> > (https://covid.postera.ai/covid <https://covid.postera.ai/covid>)
> > elicited an astonishing response...  (I confess I was quite taken aback.)
> > 
> > I just realised I should let this BB know the second call for designs is
> > now open.  Deadline is tomorrow 23:59 PST (April 2nd).  (Apologies for
> > those that weren't following on twitter.)
> > 
> > Two things:
> > we're asking for designs especially focusing on covalent inhibitors (read
> > more here
> > <https://discuss.postera.ai/t/screening-cascade-fast-track-and-regular-tr
> > ack-of-designs/567>) the most convincing designs will be fast-tracked by
> > spending more money to cut several weeks off the testing (read more here
> > <https://discuss.postera.ai/t/screening-cascade-fast-track-and-regular-tr
> > ack-of-designs/567>) Happy designing!
> > 
> > Frank
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1>
> ####
> 
> To unsubscribe from the CCP4BB list, click the following link:
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--
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University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-11 Thread Tim Gruene
Dear Gerard,

you are wrong. 'he'  in this context has as much information as 'someone' and 
'person'. It does not refer to the sex of the person spoken about. 

Best regards,
Tim

On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> >>>   Sorry to have taken this matter up in such a visible manner: I
> >>>   noticed
> >>> 
> >>> this very wrong formula in someone's paper, and that person then told me
> >>> where he had found it. Having landed on that page, I didn't know where
> >>> to go
> For the students:
> 
> "someone" = systematic absence of information = 0 bits
> "person" = systematic absence of information = 0 bits
> "he" = 1 bit of information!
> 
> --The other Gerard (1 bit of information!)
> 
> **
> Gerard J. Kleywegt
> 
>http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> **
> 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 !
> **
> 
> ############
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

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--
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University of Vienna

Phone: +43-1-4277-70202

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[ccp4bb] arpnavigator: change contour plane orientation

2020-03-07 Thread Tim Gruene
Dear all,

the arpnavigator can display the contour levels of a map ("map style plane"). 
Does anyone know how to change the orientation of the plane, i.e. the normal 
of the cutting plane?

Best regards,
Tim

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
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University of Vienna

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Re: [ccp4bb] Overrefinement considerations and Refmac5.

2020-03-07 Thread Tim Gruene
Dear TO,

at medium to poor resolution, I prefer to set the weighting myself rather than 
use the automatic weighting. At 3'ish A resolution, I would start with 0.01 or 
0.005 with many more than the default 10 cycles, maybe 50 or 100. The numbers 
you list below go in the other direction (>4).

Best,
Tim

On Friday, March 6, 2020 2:36:01 PM CET M T wrote:
> Dear BBers,
> 
> I am trying to refine a structure using COOT and Refmac5 and I have some
> concerns about overrefinement and x-ray term weight in Refmac5, based on
> the fact that during refinement to let R factor to drift too far from Rfree
> is not good...
> 
> So... First question about that : what is too far ? I have some values in
> mind like 6% of difference is OK, 10% is not... But is there a relation in
> between resolution of the structure and this difference? Should it be
> higher at lower resolution, or always around 6-7% independently of the
> resolution?
> 
> Second question is, ok, I have a too big difference, lets say 9-10%... What
> could be the reason of that and on what to play to reduce this difference?
> 
> One way I choose is to look at the x-ray term weight (even if I am totally
> sure that Refmac5 is doing things better than me), because I saw that the
> final rms on BondLength were to constraint (I have in mind that this value
> should stays in between 0.02 and 0.01).
> So I looked into Refmac log to know where was the starting point and I
> found 8.75.
> Then I tried several tests  and here are the results:
> *
> 
> R factor
> 
> Rfree
> BondLength
> 
> BondAngle
> 
> ChirVolume
> 
> Auto weighting and experimental sigmas boxes checked
> 
> 0.1932
> 0.2886
> 
> 0.0072
> 
> 1.6426
> 
> 0.1184
> 
> Weighting term at 4 and experimental sigmas box checked
> 
> 0.1780
> 0.3159
> 
> 0.1047
> 
> 8.1929
> 
> 0.5937
> 
> Weighting term at 4
> 
> 0.1792
> 0.3143
> 
> 0.1008
> 
> 7.8200
> 
> 0.5667
> 
> Weighting term at 15 and experimental sigmas box checked
> 
> 0.1783
> 0.3272
> 
> 0.2020
> 
> 1.6569
> 
> 0.9745
> 
> Weighting term at 15
> 
> 0.1801
> 0.3279
> 
> 0.2022
> 
> 12.5748
> 
> 0.9792
> 
> Weighting term at 8.75
> 
> 0.1790
> 0.3235
> 
> 0.1545
> 
> 10.5118
> 
> 0.7909
> 
> Auto weighting box checked
> 
> 0.1948
> 0.2880
> 
> 0.0076
> 
> 1.6308
> 
> 0.1176
> 
> 
> 
> *Refinement Parameters*
> [image: image.png]
> 
> So like nothing looks satisfying I decided to ask my questions here...
> 
> What do you recommend to fix my problem, which is a too large difference
> between R and Rfree?
> 
> Thank you for answers.
> 
> 
> 
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--
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University of Vienna

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Re: [ccp4bb] Hydrogens in PDB File

2020-03-01 Thread Tim Gruene
by phenix.ready_set, whereas for the Buster
> >> refinements the hydrogenate tool was used.  My understanding is that both
> >> of these eventually call the reduce tool from MolProbity. 
> >> Unsurprisingly,
> >> the presence of hydrogens on the model led to both better model geometry
> >> and lower R-factors, although at these resolutions there is no observable
> >> density for the vast majority of the H-atoms in any of the refined maps.
> >> 
> >> Because the presence of the hydrogens improved the model, I have decided
> >> to
> >> leave the hydrogens at their refined positions for deposition.
> >> 
> >> I do want to point out one thing for readers interested in this topic:
> >> based on all the replies I received, there are a number of differing
> >> opinions (and therefore different practices) as to whether hydrogens
> >> should be included in deposited structures.  The expressed opinions
> >> ranged from the ethical (if the hydrogens were there for refinement,
> >> then it’s only fair that they be present in the deposited structure so
> >> that downstream users know what went into generating the reported
> >> statistics) to the practical (if the paper’s conclusions don’t rely on
> >> any arguments based on hydrogen atom positions, then there’s no
> >> compelling reason for them to be there; include them or don’t, it
> >> doesn’t matter.)  Because opinions seem to vary, perhaps it would be
> >> worthwhile for the PDB to issue some guidance on the matter for the
> >> future.
> >> 
> >> Have a nice weekend, everyone.
> >> 
> >> Matthew
> >> 
> >> ---
> >> Matthew J. Whitley, Ph.D.
> >> Research Instructor
> >> Department of Pharmacology & Chemical Biology
> >> University of Pittsburgh School of Medicine
> > 
> > 
> > 
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Re: [ccp4bb] MX data processing with GPUs??

2020-02-18 Thread Tim Gruene
Dear Ana,

you may want to check how many single board computers (like the Raspberry Pi 
or true open source hardware platform) you can buy for a single GPU high end 
graphics card. 
It may be cheaper at better performance compared to GPU computing.

XDS (and possibly also DIALS) can distribute its job across ssh, hence you 
only need the appropriate network connections. 

XDS wouldn't run on Raspberry Pi, although it may not be difficult to port.

Best,
Tim


On Tuesday, February 18, 2020 8:48:17 PM CET Ana Carolina de Mattos Zeri 
wrote:
> Dear all
> we have asked this of a few people, but the question remains:
> does any of you have experienced/tried using GPU based software to treat MX
> data? for reducing or subsequent image analysis? is it a lost battle?
> how do you deal with the crescent amount of data we are facing, at
> Synchrotrons and XFELs? Here at the Manaca beamline at Sirius we will
> continue to support CPU based software, but due to developments in the
> imaging beam lines, GPU machines are looking very attractive. many thanks
> in advance for your thoughts,
> all the best
> Ana
> 
> 
> 
> Ana Carolina Zeri, PhD
> Manaca Beamline Coordinator (Macromolecular Micro and Nano Crystallography)
> Brazilian Synchrotron Light Laboratory (LNLS)
> Brazilian Center for Research in Energy and Materials (CNPEM)
> Zip Code 13083-970, Campinas, Sao Paulo, Brazil.
> (19) 3518-2498
> www.lnls.br<http://www.lnls.br>
> ana.z...@lnls.br<mailto:ana.z...@lnls.br>
> 
> 
> 
> 
> 
> 
> 
> 
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Re: [ccp4bb] [3dem] [ccpem] Which resolution?

2020-02-12 Thread Tim Gruene
Hi Marin,

crystallography has long moved away from the term 'resolution', see e.g. 
https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2. It is merely a 
ballpark number, and it is good to know whether crystallographic data were cut 
at 1, 2, or 3 Angstrom, but not very important.

What counts is the interpretation of the model and conclusion that can be 
drawn on the system under study. It requires a broader understanding of 
crystallography in order to understand whether the conclusions are justified. 
Resolution plays only a minor role in this. It is more useful to take a look 
at the crystallographic map itself in order to understand.

EM is totally different from crystallography, and why would one mix concepts 
between the fields?

Best,
Tim

On Thursday, February 13, 2020 12:07:15 AM CET Marin van Heel wrote:
> Hi Tim,
> Good to hear from you!  No longer at PSI??
> See... You are already touching upon one of the logical breaking points in
> the resolutiton story...!  X-ray crystallography resolution criteria like
> R-factors make absolutely no sense outside the field of crystallography and
> of structural biology.  It is the result of a hybrid iterative optimisation
> process between the phases of a model structure and the measured amplitudes
> of a diffraction experiment!  The FRC/FSC resolution criteria, in contrast,
> are universal quality metrics not at all coupled to Cryo-EM or structural
> biology.  Using structural biology arguments like how well I see an alpha
> helix or how well I see the hole in an aromatic ring as an assessment
> criterion of whether a metric is good or not is a waste of time!  (Moreover
> filtering a map can completley change its appearance without changing its
> information contents). Even some my own (ex-)students and (ex-)postdocs
> sometimes completely miss this fundamental point. The FRC and FSC criteria
> are now used as quality metrics in all walks of image science like X-ray
> tomography and super-resolution light microscopy, fields of science where
> atomic coordinates of proteins are not an issue. The FRC / FSC functions
> are universal and very direct metrics that compare both the amplitudes and
> the phases of two independent measurements of images or 3D-densities of the
> same object. For more details, see the 2017 bioRxiv paper and references
> therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my
> #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal
> structures: the final phases - Current opinion in structural biology 10
> (2000) 259-264.
> 
> Cheers,
> Marin
> 
> On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene  wrote:
> > Dear Marin,
> > 
> > I did not read the enire thread, nor the manuscript you point at -
> > apologize
> > in case this has been discussed before.
> > 
> > What about a practical approach to determine the resolution of a cryoEM
> > map:
> > one could take a feature with scales of interest, e.g. an alpha-helix, and
> > shift and/or rotate it in steps of, say, 0.3A in several directions to
> > see, at
> > which magnitude (degree / distance) refinement does not take the helix
> > back to
> > its original position (within error margins).
> > 
> > One could also take a Monte-Carlo approach and do an arbitrary number of
> > random re-orientations of such a helix, refine, and calculate the
> > variation in
> > position and rotation.
> > 
> > This would reflect my understanding of resolution, much more than any
> > statistical descriptor.
> > 
> > Best regards,
> > Tim
> > 
> > On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:
> > > Hi Laurence,
> > > 
> > > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc
> > > are
> > > also based on the same SLOPPY STATISTICS  as are all  fixed-valued  FSC
> > > thresholds. This controversy has been ragings for a long long time and
> > 
> > the
> > 
> > > errors made were extensively described (again) in our most recent paper
> > > (Van Heel & Schatz 2017 BioRxiv:
> > > https://www.biorxiv.org/content/10.1101/224402v1) which has been
> > 
> > downloaded
> > 
> > > more than 3000 times. Further papers on the issue are in the pipeline.
> > 
> > The
> > 
> > > math BLUNDER behind this controversy is simple:  the inner product
> > 
> > between
> > 
> > > a signal vector and a noise vector is NOT zero (but rather proportional
> > 
> > to
> > 
> > > SQRT(N) where N is the length of the vectors) and cannot be left out of
> > 
> > the
> > 
> > >

Re: [ccp4bb] refinement of 0.73A data in shelxl

2020-02-07 Thread Tim Gruene
Hi Phil,

yes, you are right. I mixed up the occupancy number with the part number.

I find these things easier in front of the res-file.

Thanks a lot for correcting this.

Best,
Tim

On Thursday, February 6, 2020 10:26:51 PM CET Phil Jeffrey wrote:
> That doesn't sound right re: PART numbers
> 
> classically:
> 
> PART 1
> majority disordered atoms with FVAR/occupancy of e.g. "21." instead
> of usual "11."
> PART 2
> minority disordered atoms with FVAR/occupancy of e.g. "-21."
> PART 0
> The 21.000/-21.000 pairs makes the sum of occupancies add to 1.0, but
> the actual value of each group is defined by the second free variable.
> 
> See: http://shelx.uni-goettingen.de/shelxl_html.php#PART
> The "PART 1" atoms would not interact with the "PART 2" atoms.
> There's even an example for a disordered SER in the documentation.
> 
> PART -n is used for disorders that overlap on themselves on symmetry
> axes.  "If n is negative, the generation of special position constraints
> is suppressed and bonds to symmetry generated atoms with the same or a
> different non-zero PART number are excluded; this is suitable for a
> solvent molecule disordered on a special position of higher symmetry
> than the molecule can take".
> 
> I use PART 1/PART 2/PART 0 all the time in "small molecule world" but
> I've used PART -1 precisely once.
> 
> Phil Jeffrey
> Princeton
> 
> On 2/6/20 4:15 PM, Tim Gruene wrote:
> > Dear Matthias,
> > 
> > 
> > some developers introduce new features of their refinement programs with
> > the words " ... which has been there in SHELXL since the beginning of
> > time".
> > 
> > If you are only looking for two conformations, you are looking for the
> > combination of free variable number N with part N and part -N. In case you
> > deal with more than two conformations, take a look at SUMP (as Jon
> > suggested).
> > 
> > The use of free variables is easier to explain right at the computer, so
> > please ask a colleague near you office, who is familiar with SHELXL for
> > the
> > details.
> > 
> > Best,
> > Tim
> > 
> > On Thursday, February 6, 2020 8:10:01 PM CET Barone, Matthias wrote:
> >> Sorry if the mail was not clear. I figured that out now yes. As I wrote
> >> in
> >> the update, I found this stupid error I made and now everything looks
> >> good.
> >> 
> >> Now that I got the feeling of how shelxl works, I miss one of it's
> >> features
> >> in the pdb format, namely the possibility to link occupancies of a double
> >> confirmation to another moiety, say a water or a double confirmation of
> >> the
> >> ligand. It's there a way to use something similar like FVAR in a pdb
> >> file?
> >> 
> >> 
> >> 
> >> 
> >> Dr. Matthias Barone
> >> 
> >> AG Kuehne, Rational Drug Design
> >> 
> >> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> >> Robert-Rössle-Strasse 10
> >> 13125 Berlin
> >> 
> >> Germany
> >> Phone: +49 (0)30 94793-284
> >> 
> >> 
> >> From: bogba...@yahoo.co.uk 
> >> Sent: Thursday, February 6, 2020 5:01:14 PM
> >> To: Barone, Matthias
> >> Cc: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
> >> 
> >> 
> >> Hello, hope I can help.
> >> 
> >> 
> >> OK, so here is the disp table...
> >> 
> >> SFAC  C H CL N O
> >> 
> >> DISP $C 0.005100.00239 15.73708
> >> 
> >> DISP $H-0.20.0  0.66954
> >> 
> >> DISP $CL0.188450.21747   1035.16450
> >> 
> >> DISP $N 0.009540.00480 28.16118
> >> 
> >> DISP $O 0.016050.00875 47.79242
> >> 
> >> 
> >> If we take these coordinates...
> >> 
> >> N 30.414964   -0.1476350.11689611.00.19533
> >> 0.44341 =
> >> 
> >> H0A   20.427823   -0.1386560.12325611.0   -1.5
> >> 
> >> C 10.348035   -0.1607760.11097911.00.20723
> >> 0.28451 =
> >> 
> >> O 40.363785   -0.1741540.10290611.00.21226
> >> 0.22954 =
> >> 
> >> SG50.1773030.1012670.04057210.040000.06849
> >> 0.03024 =
> >> 
> >>

Re: [ccp4bb] refinement of 0.73A data in shelxl

2020-02-06 Thread Tim Gruene
035   -0.1607760.11097911.00.20723
>0.28451 = O 40.363785   -0.1741540.10290611.0   
> 0.212260.22954 = SG50.1773030.1012670.040572   
> 10.040000.068490.03024 = O 40.2413040.071735   
> 0.03856710.960000.149820.12755 =
> 
> And here are some atoms of the inhibitor:
> 
> OBM   50.3251700.4417900.18177711.00.42576   
> 0.30731 =  <- oxygen CE1   1   -0.0364970.2621770.187030   
> 11.00.120560.22455 =  <- carbon HE1   2   -0.0288980.247344
>0.18766311.0   -1.2 <- proton NAY   40.107745   
> 0.3877040.21097211.00.167190.14264 = <- nitrogen CLAA  
> 3  0.028744999  0.27121   0.199305996 0.5<- Chloride
> 
> Turned out that Jon had a good feeling about the swapping of the lines and I
> did not understand Tim's comment "The scattering factor is derived from the
> number next to the name." Once I adjusted the numbers in the second column
> of my inhibitors to match the DISP list numbering, Rfree dropped to 16.96%
> and the map looks notably better (see attached snap shot).
> 
> 
> Again, thank you very much for such an incredible feedback.
> 
> Best, Matthias
> 
> 
> 
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> From: CCP4 bulletin board  on behalf of Tim Gruene
>  Sent: Tuesday, February 4, 2020 9:24:24 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
> 
> Dear Jon,
> 
> in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you
> like. The scattering factor is derived from the number next to the name.
> The name is just that, and identifier.
> 
> Best,
> Tim
> 
> On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc-
> 
> requ...@jiscmail.ac.uk wrote:
> > Remembered earlier that if the "CL" is not shifted one place to the left,
> > Shelx and probably most other programs treat it as carbon, i.e. its
> > assumed
> > to have 6 rather than 17 electrons. Trust occupancies OK, too ;-?
> > 
> > 
> > Jon Cooper
> > 
> > 
> > On 3 Feb 2020 18:26, "Barone, Matthias"  wrote:
> > 
> > 
> > Hi Pavel
> > 
> > glad you write me. I was hoping you would read my post.
> > 
> > - Yes, protons are added, both on the protein as well as on the molecule
> > 
> > - I initially only refined protein and ligand anisotropically, now Im
> > running a refinement with all atoms anisotrp except Hs. This would then
> > also be the same as shelxl is doing.
> > 
> > - Alternate conformations are modeled, also on the ligand. There are
> > plenty, sure, but I think I got most of them.
> > 
> > - I already used Water update during refine, there are some NO3s in the
> > structure. I got them in. There is a second ligand somewhere as artifact.
> > its density is not well defined, so I hope to get that in once the map
> > clears up more.
> > 
> > - I let phenix.refine optimize adp and chemisty weights, but as Petri
> > suggested, Im manually increasing the scale factors to match the ones from
> > shelxl (just to compare them properly). Im aiming for an rsmd of
> > 0.02-0.03A
> > like Petri suggested and keep an eye on how tight the structure is refined
> > in shelxl.
> > 
> > 
> > 
> > 
> > About the Rfact and the gap. Yes, thats what I was expecting. I hope if I
> > add more anisotropic B fact, the Rfacts should go down to at least what
> > shelxl yielded.
> > 
> > 
> > 
> > 
> > thank you all again for the massive feedback, ideas and help.
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > Dr. Matthias Barone
> > 
> > AG Kuehne, Rational Drug Design
> > 
> > 
> > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> > Robert-Rössle-Strasse 10
> > 13125 Berlin
> > 
> > Germany
> > Phone: +49 (0)30 94793-284
> > 
> > 
> > From:Pavel Afonine 
> > Sent:Monday, February 3, 2020 7:14:25 PM
> > To:Barone, Matthias
> > Cc:CCP4BB@JISCMAIL.AC.UK
> > Subject:Re: [ccp4bb] refinement of 0.73A data in shelxl
> > 
> > Hi Matthias,
> > 
> > 
> > did you use correct model parameterization and opt

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

2020-02-05 Thread Tim Gruene
ma Iberoamericano
> de Ciencia y Tecnologia para el Desarrollo (CYTED) through de MICROBES
> consortium.
 
> Organizers:
> Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay
> Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United
> Kingdom
 Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP,
> Brazil 
> Applicants:
> 25 students will be selected, prioritizing advanced PhD, postdocs and young
> researchers. The Course will provide financial support covering
> registration fees, and for the case of those students coming from abroad,
> all local expenses (lodging, per diem and local transportation). Look in
> the www site for details on application procedures.
 
> The application deadline is July 9, 2020.
> 
> Please address further inquiries to:
> mx2...@pasteur.edu.uy<mailto:mx2...@pasteur.edu.uy>
 
> Looking forward to hosting you in Montevideo!
> 
> 
> 
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--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

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Re: [ccp4bb] refinement of 0.73A data in shelxl

2020-02-04 Thread Tim Gruene
hat contains the inhibitor. Hence, I used pdb2ins and the pdb from PRODRG
> to produce SFAC for the inhibitor Cloride. I then pasted this line
> 
> 
> DISP $CL0.188450.21747   1035.16450
> 
> 
> 
> into the .res file and updated the UNIT line. Shelxl runs through, and the
> density looks ok on the Chloride now. However Rfree is back up at 24% and
> the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): now,
> very distincitvly, backbone carbonyls and NHs show difference density.
> 
> Am I right in my assumption, that the SFAC of Cloride is not properly
> calculated at the given wavelenght? And if so, how do I guess it correctly?
> 
> 
> 
> 
> 
> Thank you very much for your help!
> 
> Best, matthias
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
> 
> 
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--
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University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] Protein concentration for the initial crystallisation trials

2020-01-08 Thread Tim Gruene
Dear Armando,

in case you have enough material to spare, I would use a concentrator to 
create a saturated solution, i.e. concentrate until it precipitates. Measure 
the concentration of the saturated solution, i.e., supernatant without 
disturbing the solution with the precipitate.

You can start crystallisation trials at 70-90% of this concentration.

Best,
Tim

On Wednesday, January 8, 2020 5:16:31 PM CET Armando Albert wrote:
> Dear all,
> I was wondering how to guess the optimal protein concentration for the
> initial crystallisation trials. Is there any trick or assay other than the
> classic PCT from Hampton? Armando
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] 8/ 2263 spots indexed XDS

2019-11-29 Thread Tim Gruene
Dear Almudena,

SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to 
increase in your situation. The default is 3. Try e.g. 5, and increase slowly 
to make sure that the suggested solution makes sense

Best regards,
Tim

On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra wrote:
> Dear all,
> 
> I have some data sets that don't want to be processed :p
> 
> In one of them, when I look at IDXREF.LP I see virtually none of the found
> spots were indexed and the reason is that they are "too far from the
> expected position". The spots are smeary and elongated, so not the
> prettiest.
> 
> I have managed to process so far only one data set with decent statistics
> from another crystal harvested from the same drop, where the diffraction
> spots look better.
> 
> I am trying to find in the xds wiki the keyword I should fine tune in order
> to make those spots indexable.
> 
> Could you help me please?
> 
> Thank you very much in advance.
> 
> Best wishes,
> 
> Almu
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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--
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Faculty of Chemistry
University of Vienna

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Re: [ccp4bb] Shelx and debian 10

2019-10-08 Thread Tim Gruene
hared library:
> > [libgfortran.so.3]
> >  0x0001 (NEEDED) Shared library: [libm.so.6]
> >  0x0001 (NEEDED) Shared library: [libgcc_s.so.1]
> >  0x0001 (NEEDED) Shared library: [libc.so.6]
> >  0x000f (RPATH)  Library rpath: [$ORIGIN/../lib]
> 
> Note the special token "$ORIGIN", which means the directory containing
> the executable (this is documented in the 'man' page for ld.so). The
> RPATH item is set to the above value with an option like
> '-Wl,-rpath,\$ORIGIN/../lib' (where the '$' character needs to be
> escaped from the shell, obviously).
> 
> Note that -rpath is not the same as -L: -L is used at link-time to find
> the libraries needed to check that all the symbols are resolvable.
> -rpath is used to locate shared libraries at run-time: its argument
> doesn't even have to exist at link-time. If you go down this route, you
> will need to specify both -L and -rpath.
> 
> > What do users think?
> 
> As for which is the best approach, I'll let others make their opinions
> known, but I hope that this explanation has helped.
> 
> Regards,
> 
> Peter.
> 
> > Best wishes, George
> > 
> > On 08.10.19 11:04, Peter Keller wrote:
> >> HI Tim,
> >> 
> >> On Mon, 7 Oct 2019, Tim Gruene wrote:
> >>> Date: Mon, 07 Oct 2019 23:04:28 +0200
> >>> From: Tim Gruene 
> >>> To: Peter Keller 
> >>> Cc: CCP4BB@jiscmail.ac.uk
> >>> Subject: Re: [ccp4bb] Shelx and debian 10
> >>> 
> >>> 
> >>> 
> >>> @Peter: are you sure that without 'vsyscall=emulate' linux binaries
> >>> need to be
> >>> dynamically linked? I would be very surprised if the linux kernel would
> >>> disable statically linked binaries. I rather think that the vanilla
> >>> versions
> >>> of shelx c/d/e (from shelx.uni-goettingen.de) are compiled with an
> >>> obsolete
> >>> compiler / obsolete compiler options.
> >> 
> >> You're right, I wrote my reply to Bernhard too rapidly, and conflated
> >> two separate issues. Debian 10 still supports static binaries of
> >> course, but in its default configuration (without vsyscall=emulate),
> >> those static binaries must be linked with a version of glibc that
> >> doesn't require vsyscalls. OTOH, dynamic binaries don't suffer from
> >> this problem, because they can use vDSO provided by the running
> >> (rather than the build) system.
> >> 
> >> I think that part of the problem is that traditionally when we want
> >> to build portable linux binaries, we tend to build on the oldest
> >> distribution that we want to support, relying on backwards
> >> compatibility to provide the portability that we are after. We often
> >> build statically, because it is a robust way of including all the
> >> required libraries and is less fiddly and error-prone than providing
> >> them as dynamic libraries. There is also no danger of breakage caused
> >> by rogue values of LD_LIBRARY_PATH (which users shouldn't be setting
> >> of course, but we have no way of stopping them). The drawback of this
> >> approach is that when backwards compatibility is broken, there is no
> >> application-level fix.
> >> 
> >> These kinds of problems are rare, but when they do happen the onus is
> >> on those of us who distribute binary applications to find solutions.
> >> Some sysadmins may have good reasons for being reluctant to change
> >> kernel parameters to get third-party applications to work.
> >> 
> >> Regards,
> >> Peter.
> >> 
> >>> On Monday, October 7, 2019 5:53:44 PM CEST Peter Keller wrote:
> >>>> Dear Bernhard,
> >>>> 
> >>>> We had this issue drawn to our attention last year by an early adopter
> >>>> of Debian 10 while it was still in testing. I thought that it was a
> >>>> bug,
> >>>> and submitted a report accordingly here:
> >>>> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=889965>. I was told
> >>>> that it is not a bug, but a feature ;-)
> >>>> 
> >>>> If you are able, you could try setting the kernel parameter
> >>>> vsyscall=emulate. In the longer term, SHELXC/D/E will have to be
> >>>> rebuilt
> >>>> to support systems where the vsyscall has been disabled. This means
> >>>> they
> >>>> ha

Re: [ccp4bb] Shelx and debian 10

2019-10-07 Thread Tim Gruene
Dear Bernhard,

as Peter mentioned, you need to reboot the system with the kernel parameter 
vsyscall=emulate. On Debian, you edit the file

/etc/default/grub 

and modify the value of 
GRUB_CMDLINE_LINUX_DEFAULT="quiet vsyscall=emulate"

(default here is GRUB_CMDLINE_LINUX_DEFAULT="quiet")

Once saved,you run the command 'update-grub' and reboot the system.

@Peter: are you sure that without 'vsyscall=emulate' linux binaries need to be 
dynamically linked? I would be very surprised if the linux kernel would 
disable statically linked binaries. I rather think that the vanilla versions 
of shelx c/d/e (from shelx.uni-goettingen.de) are compiled with an obsolete 
compiler / obsolete compiler options. 

Best regards,
Tim


On Monday, October 7, 2019 5:53:44 PM CEST Peter Keller wrote:
> Dear Bernhard,
> 
> We had this issue drawn to our attention last year by an early adopter
> of Debian 10 while it was still in testing. I thought that it was a bug,
> and submitted a report accordingly here:
> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=889965>. I was told
> that it is not a bug, but a feature ;-)
> 
> If you are able, you could try setting the kernel parameter
> vsyscall=emulate. In the longer term, SHELXC/D/E will have to be rebuilt
> to support systems where the vsyscall has been disabled. This means they
> have to be dynamic executables that include the following in the output
> of 'ldd':
> 
> % ldd /bin/bash
>  linux-vdso.so.1 (0x7fff50952000)
>  
> 
> All current distros use vDSO, so this shouldn't cause portability
> problems by itself, but handling dynamic executables can be trickier
> than static ones.
> 
> For a little more background, see <https://lwn.net/Articles/446528/>
> 
> Finally, you have my commiserations: although this change has been a
> long time coming, it hasn't attracted a lot of attention. It was bound
> to catch users of static executables by surprise.
> 
> Regards,
> 
> Peter.
> 
> On 07/10/2019 16:05, Bernhard Rupp wrote:
> > Hi Fellows,
> > 
> > we updated to Debian 10 on the local workshop computers, and reinstalled
> > 
> > Coot and ccp4. All fine.
> > 
> > Problem: Shelxc/d/e/  does not run, and
> > 
> > the call exits immediately sans any message.
> > 
> > This holds for the binaries included in ccp4 as well as for those from
> > the SHELX site.
> > 
> > The executables from CCP4 and SHELX site – same file size, probably
> > same - run fine under Debian 9.
> > 
> > I suspect a library problem.
> > 
> > Does some kind soul have CDE binaries for Debian 10 to share?
> > 
> > Many thx in advance, BR
> > 
> > --
> > --
> > 
> > Bernhard Rupp
> > 
> > Department of Genetics and Pharmacology
> > 
> > Institute of Genetic Epidemiology
> > 
> > Medical University Innsbruck
> > 
> > Schöpfstrasse 41
> > 
> > A 6020 Innsbruck – Austria
> > 
> > +43 (676) 571-0536
> > 
> > bernhard.r...@i-med.ac.at
> > 
> > --
> > --
> > 
> > k.k. Hofkristallamt
> > 
> > San Diego, CA 92084
> > 
> > 001 (925) 209-7429
> > 
> > b...@ruppweb.org
> > 
> > b...@hofkristallamt.org
> > 
> > http://www.ruppweb.org/
> > 
> > ---
> > 
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] Rfree from another mtz file

2019-09-16 Thread Tim Gruene
Dear Mariana,

you can simply create a new set for Rfree, independently of the previous one. 
It will be as good as the copied one, and there is no reason why you would 
need to maintain the same flags. As Ian Tickle explained only briefly ago, 
your new data set will have new, independent errors.

Best regards,
Tim

On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote:
> Dear all,
> 
> We tried to use the Rfree set from a lower resolution data with a higher
> resolution from the same Crystal. To do so We used aimless at ccp4i with
> the option use free flag from another mtz file and extend the data.
> 
> I think it worked, but now we don't know how to be sure we have the same
> Rfree set. Does anyone have a way to prove it?
> Thank you in advance,
> Best,
> Mariana
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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--
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Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] AW: [bruker-axs] cbf to sfrm

2019-08-29 Thread Tim Gruene
Dear Holger,

thanks a lot for the prompt reaction! This will be very useful, in particular 
in case of proper twins.

I look forward to the update,

Tim

On Thursday, August 29, 2019 11:32:00 AM CEST bruker-...@lists.wisc.edu wrote:
> Dear Tim,
> 
> 
> 
> Thanks for having brought the bug to our attention. It got fixed in the
> PROTEUM3/APEX3 2019.1 version which will be available for download next
> week.
> 
> 
> 
> Cheers,
> Holger
> 
> 
> Dr. Holger Ott
> Global Application Coordinator SC-XRD & Senior Application Scientist
> Chemical Crystallography
> 
> Bruker AXS GmbH
> Oestliche Rheinbrueckenstr. 49
> 76187 Karlsruhe, Germany
> 
>  Phone: +49 721 50997-5628
>  Fax: +49 721 50997-45628
> 
>   Holger.Ott@bruker<mailto:Holger.Ott@bruker>.com
>   www.bruker.com<http://www.bruker.com/>
> 
> 
> 
> 
> 
> Sitz der Gesellschaft/Registered Office: Karlsruhe, HRB 107524 Amtsgericht
> Mannheim, Umsatzsteuer-Ident.Nr. DE812037551, Geschäftsführer/Managing
> Directors: - Dr. Frank Burgäzy, Dr. Klaus Gohlke
> 
> Diese E-Mail einschließlich etwaiger Anlagen kann vertrauliche Informationen
> enthalten. Sie ist daher vom Adressaten vertraulich zu behandeln und darf
> nicht veröffentlicht werden. This email, including possible attachments,
> may contain confidential information. It should therefore be treated as
> confidential by the addressee and may not be published.
> 
> 
> 
> 
> 
> -Ursprüngliche Nachricht-
> Von: bruker-...@lists.wisc.edu [mailto:bruker-...@lists.wisc.edu]
> Gesendet: Sonntag, 28. Juli 2019 18:25
> An: bruker-...@lists.wisc.edu; ccp4bb@jiscmail.ac.uk;
> pheni...@phenix-online.org Betreff: [bruker-axs] cbf to sfrm
> 
> 
> 
> Dear all,
> 
> 
> 
> recently the conversion from CBF to SFRM frame format with APEX was
> discussed on the Bruker mailing list ("Synchrotron data with Bruker
> Software"), including a potential bug that parameters in the frames other
> than the first frame are not set correctly. The workaround to re-convert
> from SFRM to SFRM a second time did not help in my case.
> 
> 
> 
> I therefore updated my program sfrmtools, available at https://
> homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/
> 
> 
> 
> With the option '-u',you can provide the first frame of the run, and via
> '-p'
> 
> a parameter file that contains the critical parameters (see documentation at
> above URL) to update the header for all frames in this run. In case you
> have twinned data and want to benefit from SAINT, this should be possible
> with this feature.
> 
> 
> 
> Both 64bit Linux binary and the source code are available. The program has
> no dependencies and should compile under any platform.
> 
> 
> 
> I did not debug this new feature very thoroughly, but it worked for me so
> far.
> 
> Any bug reports are welcome to this address
> tim.gru...@univie.ac.at<mailto:tim.gru...@univie.ac.at>
> 
> 
> 
> I hope this is helpful for one or two users.
> 
> 
> 
> I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM
> header format.
> 
> 
> 
> Kind regards,
> 
> Tim
> 
> 
> 
> cc Bruker mailing list, CCP4BB, phenixBB
> 
> --
> 
> --
> 
> Tim Gruene
> 
> Head of the Centre for X-ray Structure Analysis Faculty of Chemistry
> University of Vienna
> 
> 
> 
> Phone: +43-1-4277-70202
> 
> 
> 
> GPG Key ID = A46BEE1A

-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

2019-08-01 Thread Tim Gruene
Dear Ernst,

depositing raw data would add about 100 Bytes of storage per structure to the 
RCSB, about the length of a DOI. This is because there are existing 
repositories for data storage: data.sbgrid.org (only data related to an 
already published manuscript), zenodo.org, and a few more.

They may not have the capacity for serial crystallography data sets, but for 
the typical data set, they should be sufficient.

In neither case to depositors have to pay.

Best regards,
Tim

On Thursday, August 1, 2019 9:48:40 AM CEST Schonbrunn, Ernst wrote:
> I totally agree with the deposition of raw data along with the coordinate
> set(s).  It is the only way to independently validate a model that has been
> generated by somewhat subjective procedures of data reduction and scaling,
> structure solution and refinement.
 
> More importantly, algorithms and procedures steadily evolve, thanks to you
> folks.   Raw data of important structures re-processed using future (or
> present) algorithms may result in much clearer pictures of
> structure-function relationships than those of original interpretations.
 
> What would be the best way to deposit raw data?  How much would this add to
> the storage and maintenance capabilities of RCSB?  Likely requires
> additional funding.  If grant opportunities exist one could make a strong
> case.
 
> Ernst
> 
> 
> 
> From: CCP4 bulletin board  On Behalf Of Kay
> Diederichs
 Sent: Thursday, August 1, 2019 1:54 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: EXT: Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not
> relevant
 
> First of all, you are of course correct, Rmerge (as Rmeas, Rpim, CC1/2,
> I/sigma ...) is not detector-dependent.
 
> Second, when looking at the "experiment" section of the PDB deposition, I
> note that some Rmerge values are even given there! The statistics there are
> dubious, e.g. seemingly the I/sigma in the high resolution shell is 2.2
> meaning that they could have used higher resolution data.
 
> Third, look at the sliders on the entry page: the validity of this PDB entry
> is suspicious - quite bad Rfree and geometry.
 
> One more case for the deposition of raw data. In my eyes, the RCSB policy
> should be that raw data must be deposited when accepting such a bad entry.
> 
> HTH,
> Kay
> 
> On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane
> mailto:wesl...@gmail.com>> wrote:
 
> 
> >I was looking at the following structure in the PDB:
> >http://www.rcsb.org/structure/6HR5<http://www.rcsb.org/structure/6HR5> I
> >noticed that the R/Rfree stats were pretty high for 2.9A resolution so I
> >followed up by looking for the "Table 1" statistics in the journal
> >article. Link to article:
> >https://www.nature.com/articles/s41589-019-0311-9<https://www.nature.com/a
> >rticles/s41589-019-0311-9> Table is located in the supplemental materials
> >"Table 9".
 
> >From the processing statistics it's clear that the diffraction from that
> >crystal wasn't great but I don't want to get hung up on the processing or
> >the validity of the structure. What struck me what this little explanation
> >the authors included to explain the outlier statistics in the table:
 
> >"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge data
> >are not relevant."
 
> >We all know that Rmerge isn't a great metric for data quality but I've
> >never heard that it's detector-dependent. This doesn't make sense to me.
> >If it's actually true can someone explain, please?
 
> >Thanks!
> >
> >Wes
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<https://www.j
> >iscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1>
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> scmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1>
 
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> im

[ccp4bb] cbf to sfrm

2019-07-28 Thread Tim Gruene
Dear all,

recently the conversion from CBF to SFRM frame format with APEX was discussed 
on the Bruker mailing list ("Synchrotron data with Bruker Software"),  
including a potential bug that parameters in the frames other than the first 
frame are not set correctly. The workaround to re-convert from SFRM to SFRM a 
second time did not help in my case.

I therefore updated my program sfrmtools, available at https://
homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/

With the option '-u',you can provide the first frame of the run, and via '-p' 
a parameter file that contains the critical parameters (see documentation at 
above URL) to update the header for all frames in this run. In case you have 
twinned data and want to benefit from SAINT, this should be possible with this 
feature.

Both 64bit Linux binary and the source code are available. The program has no 
dependencies and should compile under any platform.

I did not debug this new feature very thoroughly, but it worked for me so far. 
Any bug reports are welcome to this address tim.gru...@univie.ac.at

I hope this is helpful for one or two users.

I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM 
header format.

Kind regards,
Tim 
 
cc Bruker mailing list, CCP4BB, phenixBB
-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] Resonant Scattering Directionality

2019-07-26 Thread Tim Gruene
Dear Jacob,

closely related to Ethan's explanation, but not quite the same, the 
contribution of f' and f" is still affected by the fall off from the ADPs, i.e. 
they also fall off exponentially, even for high quality crystals with a very 
low B-factors.

The effect that you describe, however, still has to be accounted for during 
refinement, which is why you have the DISP command in SHELXL.

Best,
Tim

On Thursday, July 25, 2019 8:23:34 PM CEST Keller, Jacob wrote:
> Dear Crystallographers,
> 
> It seems to be a usual assumption that anomalous scattering is essentially
> angularly-independent, e.g.:
> 
> http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm
> 
> But why the can't we see anomalous-only spots at e.g. 1 Ang resolution in a
> 2 Ang data set?
> 
> This actually has some repercussions for a non-x-ray (but still resonance)
> idea, so it would be helpful to know...
> 
> All the best,
> 
> Jacob
> 
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> Desk: (571)209-4000 x3159
> Cell: (301)592-7004
> +
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Re: [ccp4bb] RES: [ccp4bb] Se-SAD phasing

2019-07-19 Thread Tim Gruene
Dear Mario,

you probably want to run more than NTRY 1000. With today's computers, NTRY 
5000 or NTRY 1 should not take very long.

You high resolution cut-off in shelxd, 2.7A, is the default, as shelxc adds 
0.5A to the high resolution limit of the full data set. In your case this 
seems reasonable, as CC(1/2) drops below 30% at about 2.75A. 

You are looking for Se incorporated into SeMet, i.e. your scatterers cannot 
have a special position. Set the second number of MIND to e.g. 3.5 (>0!) to 
reject the possibility that heavy atoms have special positions.

The main reason. why you may not have found a solution could the the FIND 8 
command. This tells shelxd to look for 8 Se-atoms. You describe yourself that 
you are expecting 80-120 Se-atom. So set with FIND 100

I strongly recommend using the GUI hkl2map by Fabio Dall'Antonio, http://
webapps.embl-hamburg.de/hkl2map/ It guides your very well through the steps of 
shelx c/d/e 

As for the space group, your indexing in XDS looks reasonable, I don't think 
that XDS accidentally doubled one of the unit cell axes.

However, from pointless.log, the decision for the 2(1) b-axis is based on 26 
reflections. I would normally trust pointless, and expect that you get as 
solution by properly setting the parameters in shelxd and trying autobuilding 
in shelxe (your resolution limit for shelxe is probably 1.9-2.0; 2.2 was quite 
a cautious resolution cut-off).

However, you may want to re-run the CORRECT steps with
SPACE_GROUP_NUMBER=16
UNIT_CELL_CONSTANTS= 118.836 167.150 151.908 90 90 90   
REIDX= -1 0 0 0  0 0 1 0  0 1 0 0

and run shelx c/d/e with spacegroup P2(1)2(1)2

(sorry, I am not sure wether conventionally a Sure, it follows attached. I am also attaching the pointless log and
> IDXREF.LP from xds.
 
> -Mensagem original-
> De: Tim Grüne  
> Enviada em: quinta-feira, 18 de julho de 2019 13:06
> Para: Mario Tyago Murakami 
> Cc: CCP4BB@jiscmail.ac.uk
> Assunto: Re: [ccp4bb] Se-SAD phasing
> 
> Dear Mario,
> 
> you may want to post the shelxc log file and the shelxd input file to get a
> bit more quantitative advice with shelxd.  For the spacegroup, it is worth
> reading the pointless log file carefully about how many expected absences
> you have per screw axis, although pointless is quite careful and does not
> suggest a screw axes when the respective axis was not recorded.
 
> 
> 
>  From your CCanom, you could cut your resolution to 2.8A for shelxd (your
> native data probably goes to 2.0'ish A, by the way).
 
> Best regards,
> Tim
> 
> Am 18.07.2019 16:19, schrieb Mario Tyago Murakami:
> 
> > Dear all,
> > 
> > I am trying to solve the phases of the following SeMet data, but so 
> > far unsuccessfully. Suggestions are very welcome. Please see below 
> > some details about the case.
> > 
> > The statistics below is from a merged data from  different kappas of 
> > the same crystal to increase redundancy. We used the fixed energy
> > 12675 eV since the fluorescence detector was not working at the used 
> > beamline to get best energy values for this crystal.
> > 
> > Xtriage did not indicate any crystallographic pathology, except 
> > moderate anisotropy.
> > 
> > The unit cells parameters are 118.72   151.82   167.05  90.000  90.000
> > 
> >  90.000 (P212121) containing from 8 to 12 molecules in the asymmetric 
> > 
> > unit. The protein has ~28.5 kDa and 10 Met residues, excluding those 
> > from the N- and C-termini, probably with low occupancy. Thus, 
> > something 80 to 120 scatterers are expected.
> > 
> > Phenix_anomalous_signal indicates a probability of 99% to solve it and 
> > the anomalous signal is theoretically in a very good range.
> > 
> > I have tried SHELXD with different resolutions and number of sites. I 
> > have also used Hyss. But all attempts failed.
> > 
> > Thanks in advance
> > 
> > Mario
> > 
> > Aviso Legal: Esta mensagem e seus anexos podem conter informações 
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Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

2019-06-05 Thread Tim Gruene
 __h>k____h >  h  k  l  FfreeF*free*
> >  1  2  3208.97  0.00174.95  0.00
> >  1  2  5226.85  0.00191.65  0.00
> >  1  2  7144.85  0.00164.86  0.00
> >  1  2  9251.26  0.00261.71  0.00
> >  1  2  11333.84  0.00335.18  0.00
> >  1  2  13800.37  0.00791.77  0.00
> >  1  2  15412.92  0.00409.90  0.00
> >  1  2  17306.99  0.00317.53  0.00
> >  1  2  19225.54  0.00220.91  0.00
> >  1  2  21101.20  1.00*  104.84  0.00
> >  1  2  23156.27  0.00156.49  0.00
> >  1  2  25202.97  0.00202.23  0.00
> >  1  2  27216.10  0.00219.28  0.00
> >  1  2  29106.76  0.00100.93  0.00
> >  1  2  31157.32  0.00154.37  1.00*
> >  1  2  3371.84  0.0020.78  0.00
> >  1  2  35179.05  0.00165.67  0.00
> >  1  2  37254.04  0.00239.96  1.00*
> >  1  2  3969.56  0.0030.61  0.00
> >  1  2  4156.20  0.0051.02  0.00
> >
> >, and awked for 1 in the free columns. Out of 6922 pairs of
> >reflections, in one case:
> >674 in the first asu (h>k) are in the free set,
> >703 in the second asu (h >only 11 pairs have the reflections in both asu free.
> >
> >out of 16011 refl in I4,
> >6922 pairs (=13844 refl), 1049 invariant (h=k or h=0), 1118 with absent
> >mate.
> >
> >out of 1601 free reflections:
> >On average 15 free reflections were in pairs, 212 were invariant under
> >the operator (no sym-mate) and 1374 (86%) were paired with working
> >reflections.
> >
> >Then do 10 more runs of 50 macrocycles with:
> >  use_lattice_symmetry = False
> >  collecting the same statistics
> >(also scripted in multirefine.csh)
> >
> >Finally, use ref2chr.eff to refine (as previously mentined) a monomer
> >in I422 (2chr.pdb) 10 times with 10% free, 50 macrocycles (also scripted
> >in multirefine.csh)
> >
> >   
> >
> >
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[ccp4bb] PhD position in electron crystallography

2019-05-09 Thread Tim Gruene
Dear all,

The Centre for X-ray Structure Analysis of the University of Vienna has an 
open PhD position in the field of chemical crystallography with electron 
diffraction with a focus on bioinorganic chemistry. 
The project connects directly to the recent results in electron 
crystallography published in Angewandte Chemie 
(https://doi.org/10.1002/anie.201811318) and Acta Cryst D 
(https://doi.org/10.1107/S2059798319003942).

The project focuses on the interpretability of electron diffraction data as 
electrostatic potential. An experimental determination of the electrostatic 
potential of a crystal structure opens new approaches for various chemically 
relevant question, e.g. the protonation state, oxidation state of metal 
complexes, or the nature of halogen bonds. 

The project may include interesting collaborations with pharmaceutical and 
catalytic industry partners.

Applicants for this PhD position must have experience single crystal X-ray 
diffraction including crystallographic data processing, e.g. XDS, DIALS, or 
APEX/Proteum, as well as structure refinement of chemical structures with 
SHELXL, OLEX, or equivalent. Knowledge in computing is a plus.

Applicants should send a letter of motivation, their CV, and contact details 
of at least one reference to me.

Best regards,
Tim Gruene

-- 
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Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] Coot and symmetry-related waters.

2019-05-01 Thread Tim Gruene
Dear Jon,

when you place an atom at the screen pointer, there is no symmetry that Coot 
would be able to use. You need to tell Coot. One way is to merge it with an 
existing molecule that has a valid symmetry description. Another way is to 
create a separate PDB file with the symmetry of your choice and reload it. For 
all subsequent water molecules, you can follow Eugene's suggestion and merge 
new water molecules into your 'water-PDB'.

Best,
Tim

On Tuesday, April 30, 2019 10:21:31 PM CEST Jonathan Cooper wrote:
> One thing I have wondered about Coot is when you add new waters into the
> structure and these go into a molecule called 'Pointer Atoms...', I have
> never worked out how to get the symmetry mates of these newly inserted
> waters to appear unless I eventually merge them into the same pdb file as
> the protein. As an example, here is a newly inserted water molecule (A6) in
> Pointer-Atoms close to a 2-fold: http://www.ucl.ac.uk/~rmhajc0/watersym.jpg
> Is there a trick to get its symmetry mate to appear without merging the
> pdb's? I am trying to avoid the situation where you accidentally build two
> or more waters into the same density because the symmetry mates are not
> showing and have to go through all the waters again afterwards to sort it
> out. I have checked the 'Show Symmetry' box for that molecule and I have
> tried changing the radius, etc. Any clues much appreciated.
> Jon.C.
> 
> 
> 
> 
> 
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Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] High Rfree in last Shell

2019-04-16 Thread Tim Gruene
Dear Jan,

You statistics look quite solid.

R-factors are not good criteria to judge the resolution cut-off. The weighting 
schemes in refinement programs have much improved since the late 1990s. A good 
starting point to learn more is 
Rupp's "Against Method: Table 1 -Cui Bono?", https://doi.org/10.1016/j.str.
2018.04.013

Best regards,
Tim

On Tuesday, April 16, 2019 6:57:06 PM CEST Jan van Agthoven wrote:
> Hi everyone,
> I’m trying to publish two structures at 3.1Å resolution with the following
> refinement statistics:
> 
> Resolution range (Å)   49.2-3.1 
> 49.3-3.1 Rfactor (%)   
> 24.0 (32.4)  23.4 (32.0) Rfree (%) 
> 26.6 (29.2) 
> 26.3 (31.6)
> 
> Data collection
> Completeness  100 (100) 
>   100 (100)
> 
> Redundancy6.9 (7.0) 
> 6.2 (6.3)
> 
> Molecules in asymmetric unit  1 
> 1
> 
> Average I/σ 14.1 (1.7)  
>  15.3 (2.0)
> 
> Rmerge (%)  14.9 (100)  
> 12.7 (100)
> 
> Rmeas (%)16.2 (100) 
>  13.9 (100)
> 
> Rsym (%)   6.2 (68.6)   
> 5.5 (57.1) Wilson B-factor 
>65.662.7
> 
> I’ve been told that the Rfree factor in the last shell are too high. Does
> anyone know how I can improve these Rfree factors other then cutting the
> resolution, which already is rather low?
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] visualising anis B factors

2019-01-23 Thread Tim Gruene
Dear Rob,

the commonly used term 'Ortep plot' and the respective entry in the Platon GUI 
make sure that at least the name of the program is not forgotten.

Best,
Tim

On Wednesday, January 23, 2019 9:07:36 PM CET Sweet, Robert wrote:
> Please remember Carrol Johnson and colleagues. In 1965 from Oak Ridge
> National Lab they released a FORTRAN program, ORTEP, that would write
> instructions for a CalComp plotter, not only to make a molecular drawing
> showing thermal ellipsoids, but also to create them IN STEREO! This program
> revolutionized crystallographic publishing, not so much for the ellipsoids,
> but for the easy visualization of ones molecules in three dimensions. It
> seems so easy now.
> 
> 
> Bob
> 
> 
> 
>   Robert M. Sweet   E-Dress:  sw...@bnl.gov
>   Deputy Director, LSBR: The Life Science and
>Biomedical Technology Research Center at NSLS-II
>   Photon Sciences and Biology Dept
>   Brookhaven Nat'l Lab.
>   Upton, NY  11973 U.S.A.
>   Phones:631 344 3401  (Office)
>  631 338 7302  (Mobile)
> 
> 
> 
> 
> From: CCP4 bulletin board  on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: Wednesday,
> January 23, 2019 1:46:29 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] visualising anis B factors
> 
> Thank you! I still love the BB
> Eleanor
> 
> On Wed, 23 Jan 2019 at 16:24, Christian Roth
> mailto:christianroth...@gmail.com>> wrote: In
> ccp4mg it is the representation tab --> Thermal ellipsoids
> 
> 
> 
> On Wed, Jan 23, 2019 at 4:51 PM Oliviero Carugo
> mailto:oliviero.car...@univie.ac.at>> wrote:
> You might be interested in Chimera too (--> Tools --> Structure Analysis
> --> Thermal ellipsoids)
> 
> On 23.01.2019 16:17, Eleanor Dodson wrote:
> > Is there any easy way to do this?
> > 
> > Coot? ccp4mg?
> > 
> > Eleanor Dodson
> > 
> > -
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
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> 
> 
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> 
> 
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Faculty of Chemistry
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Phone: tba

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Re: [ccp4bb] visualising anis B factors

2019-01-23 Thread Tim Gruene
Dear Eleanor,

in Coot, this is four clicks away from the main menu:
Draw ->Anisotropic Atoms->'Yes'->Apply

Best,
Tim

 On Wednesday, January 23, 2019 4:17:27 PM CET Eleanor Dodson wrote:
> Is there any easy way to do this?
> 
> Coot? ccp4mg?
> 
> Eleanor Dodson
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Faculty of Chemistry
University of Vienna

Email: tba
Phone: tba

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Re: [ccp4bb] hybrid photon counter in the home lab

2019-01-16 Thread Tim Gruene
Dear Wolfram,

the principles of data integration do not differ much between small molecule and
macromolecular data (XDS, DIALS, HKL2000, mosflm, and SAINT can be used for
either), hence the advantages reported for chemical crystallography should apply
likewise for macromolecular crystals.

In addition to what is listed for small molecule, the problem of overlapping
reflections due to large unit cell axis might slighlty improve with hybrid pixel
detectors, when the point spread is less than for CCD et al.

Best,
Tim


On Tue, Jan 15, 2019 at 01:20:06PM -0500, wtempel wrote:
> Hi,
> I would value your opinions in this equipment-related question.
> Allé et al have compared detector types with a molybdemon source for a
> small molecule application
> <https://dx.doi.org/10.1088/0031-8949/91/6/063001>. Are there similar
> published comparisons for protein crystallography? What benefits can I
> expect from replacing a CCD detector with a hybrid photon counter at an
> energy of 8 keV and in the absence of the flux that a modern synchrotron
> provides?
> 
> Thank you in advance.
> Wolfram Tempel
> 
> 
> 
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Re: [ccp4bb] Live stream of CCP4 Study Weekend?

2019-01-09 Thread Tim Gruene
Hi Mark,

Seriously on Twitter only?
Sic transit gloria mundi.

Best,
Tim

On Wednesday, January 9, 2019 9:50:02 AM CET Mark J van Raaij wrote:
> Good morning and happy 2019,
> 
> There was an announcement on Twitter yesterday:
> https://twitter.com/ccp4_mx <https://twitter.com/ccp4_mx>
> (second post as of writing this)
> 
> pointing here:
> https://stfc.ukri.org/about-us/our-purpose-and-priorities/requesting-informa
> tion-from-uk-research-and-innovation/webinars/
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Editor of Acta Crystallographica F, Structural Biology Communications
> http://journals.iucr.org/f/
> 
> > On 9 Jan 2019, at 09:39, Kay Diederichs 
> > wrote:
> > 
> > Good morning everybody,
> > 
> > I haven't seen any announcement about the streaming of the Study Weekend
> > ... I'd be really interested to watch and listen!
> > 
> > Any hints?
> > 
> > thanks,
> > 
> > Kay
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
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> ########
> 
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[ccp4bb] Science Mag - breakthrough 2018

2018-12-02 Thread Tim Gruene
Dear all,

crystallography provides on of the candidates for the 'breakthrough of the 
year 2018' at Science Magazin ("Rapid chemical structures"). You can make your 
pick at 
http://www.sciencemag.org/news/2018/11/choose-your-2018-breakthrough-year

Best,
Tim
-- 
--
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Tim Gruene
- persoenlich -
OSUA/204
Forschungsstrasse 111
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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

2018-11-29 Thread Tim Gruene
Dear Raquel,

when they are associated with a publication, you can publish them on 
data.sbgrid.org in the US or at zenodo.org in Europe.

Best regards,
Tim

On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L wrote:
> Dear All,
> 
> How do your labs handle long-term raw data backups? My lab is maxing out our
> 6TB RAID backup (with two off-site mirrors) so I am investigating our next
> long term solution. The vast majority of the data sets are published
> structures (i.e. processed data deposited in PDB) or redundant/unusable so
> immediate access is not anticipated, but the size of data sets is
> increasing quickly with time, so I am looking for a scalable-yet-affordable
> solution.
> 
> Would be grateful for input into various options, e.g. bigger HD/RAIDs,
> cloud backup, tape, anything else.
> 
> I will compile.
> 
> Thank you,
> 
> Raquel
> --
> Raquel L. Lieberman, Ph.D.
> Professor
> School of Chemistry and Biochemistry
> Georgia Institute of Technology
> 
> 
> 
> 
> 
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Re: [ccp4bb] transform NMR ensemble with pdbset

2018-11-08 Thread Tim Gruene
Dear Kaushik,

you could try moleman2 from the Uppsala Software Factory,
http://xray.bmc.uu.se/usf/moleman2_man.html - maybe it keeps those cards
in the PDB file.

Best,
Tim

On 11/8/18 4:23 PM, KAUSHIK H.S. wrote:
> Hello,
> 
> I want to transform (rotate+translate) structures determined by NMR.  I
> tried using pdbset from the commandline.  The program seems to remove
> "MODEL" and "TER" lines from the coordinate file.  Is there a way to
> make pdbset retain these lines? or am I missing something obvious?
> 
> I could split the ensemble into individual coordinate files, apply
> transformation and merge them back.  However, is there an easier way out?
> 
> Best wishes,
> Kaushik
> 
> 
> 
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Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-11 Thread Tim Gruene
Dear Guto,

integration programs often ignore overloads, and most of them know the
detector cut-offs. mosflm has the option to estimate the resolution of
overloaded reflections from the none-overloaded parts. This should not
be a replacement for proper collection of a low resolution data set, but
it may help you identify the source of problems.

You might also want to check your low resolution cut-off. Maybe you have
a few strong reflections that are shaded by the beam stop. If these were
integrated, and a symmetry equivalent reflection was not shaded, it will
result in a large discrepancy between those two reflections. If it is a
strong reflection, it may ruin your low resolution statistics: aimless
lists only 88 reflections in the low resolution shell.

You mentioned that the difference map does not indicate unmodelled parts
of the molecule. You may still have those, and if they cannot be
modelled, they may affect your model R values.

In case you are unsure about the space group, you could try solving the
structure with SHELXT. I have done this with a unit cell volume about
twice as big as your. Those data reflected to 0.7A resolution (which
could make a very big difference), but the data quality was quite poor
(because of a large number of overloads). SHELXT would try to find the
best matching space group within the Laue group, and you can test
several Laue groups. In my case, it took SHELXT about 10min (790s) to
solve the structure in P212121. Since you have only about 1A resolution,
you could increase the number of trials with the option '-m500'.

Best,
Tim

On 10/11/2018 10:13 AM, Guto Rhys wrote:
> Hi all,
> 
> Firstly, I’d like to say I’m really impressed with the volume, speed and 
> detail of the response that I have received. Thanks everyone.
> 
> Overloads
> Eddie, Marc, Eleanor, Harry and Misha; thanks to all for suggesting 
> collection strategies and identifying the likely issue. Yesterday, I had a 
> quick look at the images and the lower-resolution reflections do look 
> overexposed. Thanks for the offer to check the images Graeme.
> 
> Weightings and anisotropic refinement
> Wim, Matthias and Robbie; sorry I had forgotten to mention that I ran the 
> structure through pdbredo to optimise weights and already refined using 
> anistropic B-factors.
> 
> Resolution
> Tony, I have tried to be objective with choosing the resolution. Recently I 
> have naively published some structures at a lower resolution than they are. 
> Now, I pretty much only use CC1/2 in the highest resolution shell to 
> determine the resolution of my dataset, i.e. 0.3 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ and 
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/), the AIMLESS output 
> also shows the individual CC1/2 for h, k and l. Lowering the resolution might 
> give nicer-looking refinement statistics but they are unrealistic. My 
> frustration is that a culture of doing this means that when someone does try 
> to publish something at its true resolution the statics will look worse than 
> previously published structures that claim to be at the same resolution. 
> 
> Petri, I think it was the limit of the detector distance so I couldn’t 
> collect at a higher resolution :(
> 
> Thanks again,
> Guto
> 
> 
> 
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Re: [ccp4bb] preparing ellipsoidally truncated data for PDB deposition

2018-09-27 Thread Tim Gruene
Dear Kevin,

you can concatenate mmCIF files, and they still remain valid, i.e. you prepare 
two independent mmCIF files and stich them together one after the other. Every 
mmCIF file starts with "data_" followed with a unique word as identifier. 
Extraction tools usually have a keyword for which data block you want to 
extract.

That should be the cleanest way to deposit your data, as each block can have 
its own description.

Best,
Tim

On Wednesday, September 26, 2018 8:34:47 PM CEST Kevin Jude wrote:
> I am preparing to deposit several structures that I refined against
> anisotropic data that I truncated with STARANISO. I will of course be
> depositing the original data with spherical resolution limits, but it seems
> that I should also deposit the ellipsoidally truncated data that I actually
> refined against. To be clear, these are the same dataset but in the second
> case the unmerged reflections have been rescaled and I/SIGIs that fall
> outside the ellipsoid are set to empty values. I have a technical problem
> with preparing the mmcif and a broader question about presenting the data.
> 
> I've tried to create an mmcif file from my mtz using
> http://sf-tool.wwpdb.org, treating the two sets of I/sigI as two datasets.
> For some reason, in the output file the test set flags are reversed for the
> second "dataset" (whichever I choose to be second); ie, o becomes f and f
> becomes o. This is a technical problem that I can correct with a text
> editor, but still irritating.
> 
> More importantly, is there a way to distinguish in the file between the
> spherically complete dataset and the truncated dataset that was used in
> refinement in a way that is useful to future users? I have not worked with
> mmcif before and am not sure what column names are permissible, nor what
> would be recognizable to other users or software. I'm interested to hear
> the thoughts and experiences of the community on this.
> 
> Best wishes
> Kevin
> 
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
> 
> 
> 
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Re: [ccp4bb] Building libccp4 static.

2018-09-24 Thread Tim Gruene
Dear Ian,

is it possible that the element list in the for loop,
'ccp4-7.0/lib/pkgconfig/*.pc' is empty?
The error message contains ccp4-7.0-src as directory name, i.e. maybe it
helps to write

 for p in ccp4-7.0-src/lib/pkgconfig/*.pc

Best wishes,
Tim

On 09/24/2018 12:47 PM, Ian Tickle wrote:
> 
> All, I'm trying to build libccp4 statically (after all updates applied)
> on Ubuntu 18.04.1 and I get this error:
> 
> 2: /home/ian/CCP4-7.0/ccp4-7.0-src/chec: not
> foundls/triggers/pkgconf-pathfix-nt.trigger: Fixing .pc Files (correct
> path structure)
> /home/ian/CCP4-7.0/ccp4-7.0-src/checkout/devtools/triggers/pkgconf-pathfix-nt.trigger:
> 5: /home/ian/CCP4-7.0/ccp4-7.0-src/chec: not
> foundls/triggers/pkgconf-pathfix-nt.trigger:  
> /home/ian/CCP4-7.0/ccp4-7.0-src/checkout/devtools/triggers/pkgconf-pathfix-nt.trigger:
>  7:
> /home/ian/CCP4-7.0/ccp4-7.0-src/checkout/devtools/triggers/pkgconf-pathfix-nt.trigger:
> Syntax error: word unexpected (expecting "do") 
> E: /bin/sh
> /home/ian/CCP4-7.0/ccp4-7.0-src/checkout/devtools/triggers/pkgconf-pathfix-nt.trigger
> returned with an error code (2)
> *** success *** [3/3]
> 
> The
> file 
> /home/ian/CCP4-7.0/ccp4-7.0-src/checkout/devtools/triggers/pkgconf-pathfix-nt.trigger
> contains:
> 
> # REMatch: \/ccp4-7\.0\/lib\/pkgconfig\/.*\.pc
> 
> VERBOSE=1
> echo 'Fixing .pc Files (correct path structure)'
> 
> for p in ccp4-7.0/lib/pkgconfig/*.pc
> do
>  echo 'Checking '$p' for errors'
>  sed -i 's/=\/msys64/=\/c\/msys64/g' $p
>  sed -i 's/="\/msys64/="\/c\/msys64/g' $p
>  sed -i 's/-L\/msys64/-L\/c\/msys64/g' $p
>  sed -i 's/-I\/msys64/-I\/c\/msys64/g' $p
> done
> 
> Presumably there's a syntax error there somewhere.  I can't see it but
> then I'm not a Bourne shell expert.
> 
> Any ideas?
> 
> Thanks!
> 
> -- Ian
> 
> 
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Re: [ccp4bb] crystals that dont diffract :( :(

2018-08-14 Thread Tim Gruene
Dear Careina,

you could use the old crystals, that did not diffract, for microseeding
to regrew nicer crystals. Once you have them, try to use them as quickly
as possible. Three weeks can be a long time for crystals.

Storage in liquid nitrogen should not be the problem.

Best,
Tim


On 08/14/2018 11:58 AM, Careina Edgooms wrote:
> I got the most beautiful crystals I have ever seen and they don't
> diffract at all. Not poor diffraction, NO diffraction. Anyone know why
> this could be and how I can go about fixing it? I had three beautiful
> crystals and not one diffracted. I did leave them in the drop for about
> 3 weeks before harvesting and in liquid nitrogen for about a month
> before diffracting. Could that be a factor? If I regrew more beautiful
> crystals and diffracted straight away could that help?
> Careina
> 
> 
> 
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Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

2018-08-09 Thread Tim Gruene
Dear Tommi,

did you check whether you collected any reflections at all that should
be absent for the second screw axis? If there are non - which could
easily happen with low resolution, incomplete data - pointless and XDS
might be conservative and not estimate the likelihood for the second
screw-axis.

MR, however, will pick up the space group with all data, and thus be
able to tell between P2212 and P22121 whether or not you recorded
reflections that are expected to be absent.

Best,
Tim

On 08/08/2018 04:29 PM, Kajander, Tommi A wrote:
> Hi,
> Any clues why the followting happens: pointless (and just looking at the XDS 
> output) clearly tells there is one screw axis in P-ortorhombic (P2212)
> yet phaser gives the best Z-scores in P22121. (...I suspect this may be to do 
> with twinning - might be monoclinic twiined still though now processes very 
> well in P222.)
> 
> If i run the mtz after XDSCONV (ie F2MTZ) via pointless (instead of directly 
> after XDS) it also suggests this - but i suppose i am not suppose to run 
> merged data via pointless.
> 
> Thanks for comments,
> 
> Tommi 
> 
> 
> 
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Re: [ccp4bb] cell discrepancies and stuck refinement using different XDS-versions

2018-08-06 Thread Tim Gruene
Dear Sabine,

I would first take a look at the respective log-files for differences in 
parameter settings, in particular SPOT_RANGE / DATA_RANGE, 
INCLUDE_RESOLUTION_RANGE.
Start with IDXREF.LP, then proceed to COLSPOT.LP.

The relevant parameters are always listed in the header of the log-files. 
Programms like xxdiff or vimdiff are very useful to highlight the differences.

Best,
Tim

On Monday, August 6, 2018 4:50:56 PM CEST Sabine Schneider wrote:
> Dear all,
> 
> We are encountering a differences in indexing using different XDS
> versions, which results in either 2 or 4 mols/asu (SG P1; structure
> determination via MR (30% seq ID model)) and either successful
> refinement or stuck R/Rfree
> 
> - the data were collected at ESRF ID30A3 (Aiger detector) and extend to
> about 2.3A resolution (CC1/2 ~50%)
> 
> The XDS version build 20180126 (and or autoprocessing at the ESRF via
> autoproc, dials, xdsapp or grenade -> here also xds version from
> 20180126 used) gives us:
> 
> P1  38.6550.7661.11 110.057  99.945  90.197
> XDS complains and I need to use "DEFPIX INTEGRATE CORRECT"
> -> 2mols/asu, structure refines to R/Rfree of 22/25
> 
> In contrast the actual XDS-Version BUILT=20180409 results in:
> P1  39.2   51.3  116.8  86.3  82.3  89.8
> but XDS runs smoothly.
> -> 4mols/asu, tNCS, R/Rfree stuck at 28/32
> If I feed XDS with the smaller cell above, it fails.
> 
> (The smaller cell is also found by Xia2/dials via the CCP4i2 interface.)
> 
> Thus I am wondering, what are the differences between the two
> XDS-versions? (I remember vaguely that there was a tread about different
> XDS-versions, but couldn't find it..)
> 
> Cheers Sabine

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Re: [ccp4bb] data processing with split/bad crystals

2018-07-16 Thread Tim Gruene
Dear Tommi,

saint (Part of the Bruker APEX/Proteum suite) can integrate with, I think, up 
to five orientation matrices at a time. It integrates smoothly with twinabs. 
Saint seems quite sophisticated in modelling the reflection profiles from the 
different lattices.
EvalCCD (Eval15?) may be able to to similar things.

Other packages can integrate different lattices one after the other (XDS can 
do this with little effort), but they don't take into account that spots may 
be the result of overlapping reflections from different lattices.

You can check your next Chemistry department. Chances they have an APEX 
installation are quite high.

Best,
Tim

On Monday, July 16, 2018 10:55:15 PM CEST Kajander, Tommi A wrote:
> Dear All, 
> 
> I was wondering what would be the best software nowadays to try to process
> data from crystal that clearly is split or
 has a secondary set of lattice
> points (close, poor data) in the raw data - data can be processed with XDS
> (2.9-2.8 Å) but Rmerge tends to be bit high at low resolution (close to
> 7-8% depending on processing) - using XSCALE helps with the radiation
> damage correction some what. 
> Data looks like primitive orthorombic but not quite sure (also seems like it
> has one screw axis e.g. P2212 - but oddly phaser finds 
 solutions in
> P22121 also or even preferably…..). I am wondering a bit if it isn’t
> actually monoclinic. 
> Based on automated processing by Diamond pipeline XDS seems most robust -
> but any hints on such cases would
 be welcome. Of course we will try to get
> better crystal but so far no luck. 
> Thanks for comments,
> 
> Best
> Tommi
> 
> 
> 
> ---
> 
> Tommi Kajander, Ph.D.
> Structural Biology and Biophysics
> Institute of Biotechnology
> University of Helsinki
> Viikinkaari 1 (P.O. Box 65)
> 00014 Helsinki, Finland
> 
> 
> 
> 
> 
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Re: [ccp4bb] According correct space group assignment...

2018-04-20 Thread Tim Gruene
Dear Rafal,

shelxt does not require the space group, it only needs the Laue group. If it 
finds a decent solution, it'll find also the space group for you.

Best,
Tim

On Friday, April 20, 2018 3:30:36 PM CEST Rafal Dolot wrote:
> Dear CCP4BB,
> 
> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell
> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this
> size of the molecule. 11mer is rich in G, so we expect the G-tetraplex
> formation. Data were collected to almost 1 A, so it should be enough for
> trials with direct methods/ab initio solution. What I should do first to
> find correct SG and/or cell parameters?
> 
> Best regards,
> 
> Rafal

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Re: [ccp4bb] Observation:Parameter ratio

2018-02-17 Thread Tim Gruene
Dear Prem,

you also need to count the number of restraints as observations and 
constraints, which reduce the number of parameters. The number of restraints 
at this resolution might exceed the number of observations. If I remember 
correctly, the numbers are listed in the refmac5 log file and probably also in 
the PDB file header after refinement.

The difference between Rfree and R1 is a measure for overfitting, see https://
doi.org/10.1107/S0907444999016868 and https://doi.org/10.1107/
S0907444997013875

Best,
Tim

On Saturday, February 17, 2018 8:46:39 PM CET Prem Prakash wrote:
> Dear all,
> How observation is to parameter ratio is determined for a crystal
> structure. Suppose If we have only one observation for each parameter at a
> resolution of say 2.9 Angstrom, how terribly it is easy to overfitt for the
> data to get a misleading agreement between model and experiment ? Is there
> any thumbrule for this ratio, and how it is dependent on the resolution of
> the data. Please shed some light on these aspects.
> Thank you
> With kind regards
> Prem

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Re: [ccp4bb] coordinate transformation

2017-12-14 Thread Tim Gruene
Dear Tommi,

if you only need to consider translations, and not other symmetry operations, 
you can use moleman2, convert coordinates to fractional ones and add or 
substract the integer that brings the centre of mass closest to 0.

In case you want to take the symmetry operations into account, you would have 
to check for each operator, which one brings the centre of mass closest to 0. 
This could most likely be scripted with moleman2.

Best,
Tim

On Thursday, December 14, 2017 8:39:48 AM CET Kajander, Tommi A wrote:
> Dear Paul,
> 
> 
> Yes thank you. This was the best answer i think. Someone else already also
> suggested that also.  Coot is very handy indeed.
> 
> 
> (Would still be curious of knowing how to find the "closest to origin" copy
> otherwise - but this solves my problem)
> 
> 
> Thanks to all who responded.
> 
> 
> Cheers,
> 
> Tommi
> 
> 
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley
> <pems...@mrc-lmb.cam.ac.uk> Sent: Thursday, December 14, 2017 3:25:19 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] coordinate transformation
> 
> On 13/12/2017 13:50, Kajander, Tommi A wrote:
> > Hello,
> > 
> > If someone could point this out would be very helpful... Wasnt there a
> > simple script somewhere that would transfer coordinates close to origin -
> > if they for some reason are not? Just cant find anything right away.
> At the risk of not answering the question because it's not a simple script,
> my I recommend Coot?
> 
> File -> Open -> yourcoords.cif
> Draw -> Cell & Symm -> Master Switch -> Yes
> Show Unit Cells -> Yes
> OK
> Drag the View to the Origin # it's marked with an "O"
> Middle-mouse click on an Symmetry-related Atom # that's close to the origin
> Extensions -> Modelling -> Symm Shift Reference Chain Here

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Re: [ccp4bb] mmCIF and CIF

2017-11-14 Thread Tim Gruene
Dear Oliviero,

depending where the mmCIF originates from, and provided you have data with it, 
it might be easiest to go
mmCIF -> PDB -> SHELXL (via PDB2INS) -> CIF (via the SHELXL ACTA command).

Best,
Tim

On Tuesday, November 14, 2017 2:16:06 PM CET Oliviero Carugo wrote:
> Dears,
> 
> does anybody know how to transform an mmCIF file of the Protein Data
> Bank into a CIF file (the slightly different format used in small
> molecule crystallography)?
> 
> Thanks,
> 
> Oliviero

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Re: [ccp4bb] software to map surface residues

2017-11-04 Thread Tim Gruene
Dear Kai,

the output of the CCP4 program 'surface' lists the "accessible area of atom".
Without trying I'd extract those residues with a non-zero entry there.

Regards,
Tim

On Friday, November 3, 2017 8:59:03 AM CET Kai Zhou wrote:
> Hello, is there an existing program that can extract the 3D coordinates of
> the surface residues of a given protein/PDB file? Thanks so much~~
> 
> Kai
> 
> Buck Institute

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Re: [ccp4bb] mtz2hkl for shelx

2017-10-27 Thread Tim Gruene
Dear Abhishek,

this is only a warning. Your file aj83.hkl has been created, and you can use 
it.

If you would like me to look into it, you could send me the mtz-file for taking 
a look.

Best regards,
Tim

On Friday, October 27, 2017 4:31:02 PM CEST Abhishek Anan wrote:
> Dear all,
> 
> I am trying to convert mtz file processed using DIALS to hkl format for
> input into shelxL but I get the following warning about missing
> reflections.
> 
> $ mtz2hkl  aj83.mtz
> 
> *** WARNING *** WARNING *** WARNING *** WARNING *** WARNING
> **
> * 1268 reflections were flagged missing based on
> checking*
> * Data-, Sigma-, AND Rfree-column. This is greater than 1% of the
> total*
> * Reflections. Please check your hkl-file contains all the data from
> the*
> * mtz-file. One reason might be unflagged Rfree-columns, e.g. if you
> copied  *
> * the Rfree-column from a file at lower
> resolution.*
> * The simplest remedy is to run the ccp4 program FREERFLAG with the*
> * Keyword 'COMPLETE FREE=RFree_Flag
> *
> *** WARNING *** WARNING *** WARNING *** WARNING *** WARNING
> **
> 
> mtz2hkl write data: 30228 lines written
>  ** SUMMARY:
> Data:  column  13, label: "IMEAN"
> Sigma: column  14, label: "SIGIMEAN"
> Rfree: column   3, label: "FreeR_flag"
> Format: HKLF 4
> Spacegroup: P 1 21 1
> Cells present in mtz-file:
> 29.3205 26.6201 64.4701  90 92.26 90
> 29.3205 26.6201 64.4701  90 92.26 90
> 30228 reflections written to file "aj83.hkl"
> 1499 Reflections with FreeR_flag = 0 marked as test set (-1)
> 
> 
> I tried FREERFLAG suggestion but to no avail. How do I fix this?
> 
> Thank you,
> Abhishek
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Re: [ccp4bb] ccp4 website not secure

2017-10-11 Thread Tim Gruene
Dear Markus, dear Michael,

the certificate from ccp4 appears to be signed by QuoVadis Ltd. 
If I understand correctly, this is a trusted company, as of Firefox Version 
32, according to the information at https://wiki.mozilla.org/CA/
Included_Certificates

Maybe you need to UPdate, not DOWNdate your browser?

Regards,
Tim

On Wednesday, October 11, 2017 12:50:13 PM CEST R. Michael Garavito wrote:
> Markus,
> 
> I had that problem for a short while with slightly older versions of
> Firefox, but more recently (v54 - v56) it has not impacted any of the CCP4
> sites.  Whether it is a Firefox correction, I don’t know, but it is fine
> for me.  Note that CCP4online is https://www.ccp4.ac.uk/ccp4online/
> <https://www.ccp4.ac.uk/ccp4online/>, which requires logins, but ccp4 is
> http://www.ccp4.ac.uk/ <http://www.ccp4.ac.uk/> still.  I had it mostly
> when connecting from home.
> 
> Michael
> 
> 
> R. Michael Garavito, Ph.D.
> Professor of Biochemistry & Molecular Biology
> 603 Wilson Rd., Rm. 513
> Michigan State University
> East Lansing, MI 48824-1319
> Office:  (517) 355-9724 Lab:  (517) 353-9125
> FAX:  (517) 353-9334Email:  rmgarav...@gmail.com
> 
> 
> > On Oct 11, 2017, at 12:34 PM, Edward A. Berry <ber...@upstate.edu> wrote:
> > 
> > Is it because of this? Its been coming for a while now:
> > https://blog.mozilla.org/security/2015/04/30/deprecating-non-secure-http/
> > 
> > I see no reason why a website, dedicated to providing information
> > available to everyone, should be required to use https.
> > The web is too focused on e-commerce, where security is more important.
> > 
> > I hope firefox can be configured to allow insecure http, perhaps with a
> > warning. Otherwise downgrade to previous version (FF 47 connects fine).
> > Just be sure when visiting ccp4.ac.uk, don't enter personal info
> > like your tax-payer ID or credit card number. If you need to login
> > to modify the wiki or your subscription details, use another password for
> > the bank.
> > 
> > eab
> > 
> > On 10/11/2017 05:15 AM, Markus Heckmann wrote:
> >> If anyone from CCP4 website has noticed that...
> >> Your connection is not secure
> >> 
> >> 
> >> The owner of www.ccp4.ac.uk has configured their web site improperly.
> >> To protect your information from being stolen, Firefox has not
> >> connected to this web site.
> >> 
> >> 
> >> (https warning message)
> >> https://www.ccp4.ac.uk/ccp4online/

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Re: [ccp4bb] include corners in mosflm

2017-09-27 Thread Tim Gruene
Dear JPK,

the CSD holds about 8x more crystal structures than the PDB. Taking ICSD into 
account as well as many non-published structures, it is probably safe to say 
that the majority of structures did require 'swung out mode' - 'atypical' may 
be a little a narrow view of crystallography.
At many synchrotron beamlines, that often do not provide a 2theta arm, it is 
often borderline to get to the Acta Cryst C limit for publication, i.e. 0.84A 
complete data.

Best,
Tim


On Wednesday, September 27, 2017 12:09:47 PM CEST Keller, Jacob wrote:
> You’ve got a point about including data, but on the other hand, I would
> assume one would (almost always) set the collection parameters so as not to
> require use of the corners. And “swung out” mode is pretty atypical, so
> would be strange to set a default for it.
 
> JPK
> 
> From: herman.schreu...@sanofi.com [mailto:herman.schreu...@sanofi.com]
> Sent: Wednesday, September 27, 2017 2:44 AM
> To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK
> Subject: AW: [ccp4bb] include corners in mosflm
> 
> With a detector in swing-out position, one has to include the corners. Also,
> why should one discard potential data during processing? Based on the
> statistics, one can always discard data afterwards if it is not good or too
> incomplete.
 
> HS
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Keller, Jacob
 Gesendet: Dienstag, 26. September 2017 22:14
> An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: Re: [ccp4bb] include corners in mosflm
> 
> Why on earth would one want that to be the *default*? I understand that
> there may be the odd unrepeatable dataset collected too close, or there may
> be occasionally be hardward limitations, but I cannot understand how this
> would be a recurring problem….
 
> JPK
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> CCP4BB
 Sent: Tuesday, September 26, 2017 4:11 PM
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: Re: [ccp4bb] include corners in mosflm
> 
> Hi Ed
> 
> I'm afraid not; that's one thing that can't be changed to a different
> default.
 Harry
> --
> Dr Harry Powell
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
 
> On 26 Sep 2017, at 20:34, Edwin Pozharski
> <pozharsk...@gmail.com<mailto:pozharsk...@gmail.com>> wrote:
 By default,
> iMosflm excludes corners from processing.  Is there a simple way to make it
> the default to go all the way to the corner instead of detector edge?  I
> could of course set the max resolution for processing to some outrageous
> value that is guaranteed to be outside of the image, but perhaps I am
> missing a more intelligent option in the gui.  (I vaguely recall HKL2000
> having a Edge/Corner/Other) radiobutton). 
> There is a whole separate question as to wisdom of including corners, of
> course.  Yes, adding a resolution shell with robust data will improve model
> quality even if such shell is woefully incomplete. On the other hand, it's
> possible that fill-in option for missing reflections in map calculation may
> make maps more biased. A reasonable solution to this would be to use 2
> different resolution limits in refinement and map calculation - not hard to
> script for that yet I don't know if any refinement software provides such
> option natively.
 Ed.
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Re: [ccp4bb] PAK=0 problem

2017-09-22 Thread Tim Gruene
Hi James,

small molecule structures usually model every or nearly every atom in the 
asymmetric unit - do you think that simple answer is too naive?

Best,
Tim

On Friday, September 15, 2017 9:25:25 AM CEST James Holton wrote:
> You know, I've been pondering that question for most of my adult life. 
> Why can't we push macromolecular R factors down to the level of
> experimental error like our "small molecule" colleagues do routinely?  I
> have a few ideas, and others do too.  In fact, there will be session on
> this topic at the next ACA meeting.
>  [...]
> -James Holton
> MAD Scientist
> 
> On 9/15/2017 4:32 AM, rohit kumar wrote:
> > why R/Rfree not going down from 21/25?

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Re: [ccp4bb] CHAINSAW ERROR

2017-09-03 Thread Tim Gruene
Dear Vicky,

did you possibly edit this file with Word or some other text formatting 
program? A file .aln is a pure text file. What you sent is a binary file, hence 
not interpretable as alignement file.

There are proper text editors even for windows. Notepad is one option.

Best,
Tim


On Sunday, September 3, 2017 6:05:21 PM CEST Vicky Tsirkone wrote:
> Dear,
> 
> You may find attached the corresponding file.
> It does not contain the real sequences (I replaced every aa with ALA) but
> overall this is how it looks like.
> 
> Best,
> 
> Vicky
> 
> On Sun, Sep 3, 2017 at 5:53 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk>
> 
> wrote:
> > Can you attach the alignment file - there is a plethora of formats and it
> > is hard to debug them all.
> > 
> > Eleanor
> > 
> > On 3 September 2017 at 15:18, Vicky Tsirkone <vtsirk...@gmail.com> wrote:
> >> Dear all,
> >> 
> >> I faced a strange issue while I was trying to run CCP4-chainsaw. I used
> >> EBI-Clustal omega to prepare the desired alignement. Next, I copied the
> >> output into a text file and renamed it to alignment.aln. When I chose
> >> this
> >> file in chainsaw it gave me back this kind of error:
> >> 
> >> format error in ALN/Clustal file
> >> No CLUSTAL keyword
> >> 
> >> 
> >> This is the first line of my file : *CLUSTAL O(1.2.4) multiple sequence
> >> alignment*
> >> 
> >> I also typed CLUSTAL W instead of CLUSTAL O but ccp4 gave me the same
> >> error message.
> >> 
> >> Any suggestion will be appreciated.
> >> 
> >> Kindly,
> >> 
> >> Vicky

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Re: [ccp4bb] "reset" a structure before re-refinement

2017-08-20 Thread Tim Gruene
gned to the structure.  You may or
> may not be all that worried about this.  And if you are certain that
> the main chain trace is correct, then enforcing it in further analysis
> is not "bias", it is "prior knowledge".  I suppose knowing the
> difference between these two things is what science is all about.
> 
>  So, I'd say that "resetting" a structure depends on what aspect of
> the structure you're trying to test.  If you made a mistake in the
> backbone trace, or even a rotamer assignment, then doing a 0.5A jiggle
> isn't going to reset that mistake.  But if your trying to test the
> influence of data between 1.5 A and 1.4 A, then I'd say do a jiggle of
> at least half that distance.
> 
>  -James Holton
>  MAD Scientist
> 
> 
>  On 8/17/2017 8:40 AM, Robbie Joosten   wrote:
> 
>  *.EmailQuote {
> margin-left: 1.0pt;
> padding-left: 4.0pt;
> border-left: rgb(128,0,0) 2.0px solid;
> }
>   p.x_MsoNormal, li.x_MsoNormal, div.x_MsoNormal {
> margin: 0.0cm;
> font-size: 11.0pt;
> font-family: Calibri , sans-serif;
> }
> a:x_link, span.x_MsoHyperlink {
> color: blue;
> text-decoration: underline;
> }
> a:x_visited, span.x_MsoHyperlinkFollowed {
> color: rgb(149,79,114);
> text-decoration: underline;
> }
> *.x_MsoChpDefault {
> }
> div.x_WordSection1 {
> }
>In most cases resetting the B-factors
> would be enough to perturb the model.
> 
>Cheers,
>Robbie
> 
>Sent from my Windows 10 phone
> 
> From:   Andrew Leslie
>Sent: 17 August 2017 17:29
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] "reset" a structure before 
>  re-refinement
> 
> 
> 
> 
>   Hi Graeme,
> 
>  You can do this with PDBSET, keyword NOISE
>  Cheers,
> 
> 
>  Andrew
> 
>  > On 17 Aug 2017, at 16:17, Graeme Winter
>  > <graeme.win...@diamond.ac.uk> wrote:
>  > 
>  > Dear All,
>  > 
>  > Is there a protocol out there to gently perturb atomic   
>  >  positions so that re-running refinement can essentially
>  > put         them back without bias from the original
>  > refinement? In particular, if trying to perform
>  > the Karplus and Diederichs paired refinement
>  > protocol, I do not want to run the lower
>  > resolution refinements with the "memory" of the weak high   
>  >  resolution data present... and only have the
>  > refined structure to work from...
>  > 
>  > Am using refmac5, but any pdb randomizer would hit the   
>  >  spot
>  > 
>  > Many thanks Graeme

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Re: [ccp4bb] "reset" a structure before re-refinement

2017-08-18 Thread Tim Gruene
Hi Andrew,

as far as I understand, PDBSET only affects the coordinates. The WIGL command 
in SHELXL also add noise to the ADPs, which has a dramatic effect on the 
resulting R1-value. See Figure S5 A vs. S5 B in doi: 10.1073/pnas.1502136112

At least one should reset the B-values in refmac, I guess.

Best,
Tim


On Thursday, August 17, 2017 4:29:14 PM CEST Andrew Leslie wrote:
> Hi Graeme,
> 
> You can do this with PDBSET, keyword NOISE
> Cheers,
> 
> 
> Andrew
> 
> > On 17 Aug 2017, at 16:17, Graeme Winter <graeme.win...@diamond.ac.uk>
> > wrote:
> > 
> > Dear All,
> > 
> > Is there a protocol out there to gently perturb atomic positions so that
> > re-running refinement can essentially put them back without bias from the
> > original refinement? In particular, if trying to perform the Karplus and
> > Diederichs paired refinement protocol, I do not want to run the lower
> > resolution refinements with the "memory" of the weak high resolution data
> > present... and only have the refined structure to work from...
> > 
> > Am using refmac5, but any pdb randomizer would hit the spot
> > 
> > Many thanks Graeme
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[ccp4bb] Reminder: PSI / CCP4 Workshop "3D Electron Crystallography for Macromolecular Compounds"

2017-08-15 Thread Tim Gruene
Dear all,

this is a reminder of the PSI / CCP4 Workshop 

"3D Electron Crystallography for Macromolecular Compounds"

The workshop will take place at PSI between 18th and 22nd September 2017.

Please see the full program, list of speakers, and registration instructions 
at 
https://indico.psi.ch/conferenceDisplay.py?confId=5525

We extended the number of participants by 10 places. 

Please register before 1st September 2017.

On behalf of the organisers,
Tim Gruene
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Re: [ccp4bb] SHELXE: peptide occupancy refined to negative value

2017-07-11 Thread Tim Gruene
Dear Andreas,

did you try the option '-t' to make SHELXE try harder, or other building 
related options (take a look at the SHELX web page for talks and 
presentations).

Can you make use of the phases without model building? (sfall)

Since you seem to get a PDB-file, could you use the coordinates to calculate 
the phases off it? You can also provide the PDB-file as input file and restart 
phasing.

Best,
Tim

On Monday, July 10, 2017 5:51:57 PM CEST Andreas Förster wrote:
> Dear all,
> 
> since SHELX is now part of CCP4, this question is not entirely off-topic.
> 
> I'm trying to solve structures by S-SAD.  Substructure looks weak but ok if
> the right resolution cutoff is picked in SHELXD.
> 
> SHELXE is happy to do its thing for a while but then gives up with a
> "Peptide occupancy has refined to negative value" error in one hand.  The
> other hand is quite obviously (CC for partial structure, number of residues
> built) wrong, but the PDB obtained with the antimatter peptides looks like
> protein, is 80% complete and quite obviously the right solution.
> 
> Because of the error, SHELXE doesn't write phases.  How do I get these?  (I
> could do MR, but there must be a more elegant way...)  Better yet, what
> might cause the "negative occupancy" error and how do I avoid it?
> 
> Thanks and all best.
> 
> 
> Andreas
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