Re: [ccp4bb] reference for true multiplicity?

[George Sheldrick]

Dear Frank,

We did extensive testing of this approach at the beginning of this 
millenium - see

Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea.

Best wishes,
George

On 05/14/2013 06:50 AM, Frank von Delft wrote:

Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead:

Anybody know a (the) reference where it was showed that the best SAD 
data is obtained by collecting multiple revolutions at different 
crystal offsets (kappa settings)?  It's axiomatic now (I hope!), but I 
remember seeing someone actually show this.  I thought Sheldrick early 
tweens, but PubMed is not being useful.


(Oh dear, this will unleash references from the 60s, won't it.)

phx




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?

[George Sheldrick]

One day many years ago, my Ph.D. students all appeared wearing T-shirts 
with the logo
We want more redundancy. They had clearly got the message about how to 
do sulfur
SAD phasing, but were completely unaware of the usual meaning of the 
word in the UK!


George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] shelx c/d/e question

[George Sheldrick]

Dear Olga,

I always run SHELXC/D/E from hkl2map because of the nice graphical 
diagnostics while the programs are running.
If you start hkl2map, give any project name and choose 'more options' 
you will be able to specify that you need more memory.


From your comment I suspect that you are using an old single CPU 
version of SHELXD. The current version uses all available
CPUs and is much faster; it is available via 
http://shelx.uni-ac.gwdg.de/SHELX/  My reason for suspecting this is that I
changed the -L default for the multi-CPU version to allow finer control 
of the memory. otherwise it can be tricky to run the 32-bit
version with a large number of CPUs on a large structure. So for the old 
single CPU  version you probably need -L2 and for the
current multi-CPU version version -L20 when running the programs from 
the command line for your large (MAD?) problem.


I don't know how this is handled by CCP4i, but I'm sure that someone on 
this list will be able to help.


Best wishes, George

On 06/05/2013 06:39 PM, Olga Moroz wrote:

Dear All,

I am trying to run shelx c/d/e from ccp4 interface (latest updated version of 
CCP4). The program terminates with message:
Arrays too small to generate reflection data -try -L1.  (Which, as I 
understand, means I have too many reflections, and that one way around the problem
is to use lower resolution).
However, the question is - where should I put this -L1 flag from the interface? 
In the command line it would, probably,  have been shelxe -l1
But if I use a run and view command scripts option, there is no obvious place 
to put it.

Many thanks,
Olga




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Off-topic: NMR and crystallography

[George Sheldrick]

The title of my PhD thesis was NMR of inorganic hydrides but I soon 
realized that I was out of my depth with
the theory so switched to something easier to understand (gas phase 
electron diffraction). However this involved
taking the (somewhat dangerous) samples by  train to Durward 
Cruickshank's machine in Glasgow (later
Manchester). Then I managed to find a Weissenberg camera so I was able 
to do some crystallography. Two

points that don't seem to have been mentioned yet:

State of the art In-house NMR equipment is an order of magnitude more 
expensive than in-house X-ray equipment

(but of course if you need a synchrotron the real costs might be different).

Many NMR structures are more modelled than experimentally determined, 
the number of independent experimental
data can be quite small. But the good news is that force fields and 
modelling software are improving.


George

On 06/09/2013 08:12 PM, Ethan Merritt wrote:

On Sunday, 09 June 2013, Theresa Hsu wrote:

Dear all

A question for the cross-trained members of this forum - for small sized 
proteins, is NMR better than crystallography in terms of data collection 
(having crystals in the first place) and data processing? How about membrane 
proteins?

A relevant study is the comparison by Yee et al (2005) JACS 127:16512.
   http://pubs.acs.org/doi/abs/10.1021/ja053565+

They tried to solve 263 small proteins using both NMR and crystallography.
43 only worked for NMR
43 only worked for X-ray
21 could be solved either way

So you could say it was a toss-up, but consider that
- As the size gets larger, NMR becomes increasingly impractical
- 156 (60%) weren't solved by either NMR or crystallography.
   What is the relative cost of the failed attempt?

Ethan




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] OT: (a bit) shelx(pro)

[George Sheldrick]

Dear Peter,

i am planning to produce a new pdb2ins containing several improvements, 
but until this is ready please continue to use the old shelxpro.


Best wishes, George

On 17.06.2013 16:57, Peter Moody wrote:

At the risk of (more) people pointing at me and laughing...

I used to use SHELXPRO to get my .ins files sorted for SHELX, but that 
seems to have gone.


How is it done now?

I want to do a full-matrix refinement to get ESUs on some (specific) 
atoms and as far as I can remember SHELXL is the best way to go.


Any advice gratefully received, if its RTFM, then a refernce/link to 
th right page would be nice.


best wishes, Peter




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] mmCIF as working format?

[George Sheldrick]

The flexibility of CIF is indeed infinite. Even the names of the 
unit-cell dimsnsions are different in mmCIF and (small molecule) core CIF.
One of the main reasons why I had to bring out a new version of SHELXL 
recently (SHELXL-2013 to replace SHELXL-97) was that in the

meantime COMCIFS committee had changed many of the names.

George



meantime the COMCIFS committee of the IUCr had changed many of the names.


On 08/07/2013 10:02 PM, Nat Echols wrote:
On Wed, Aug 7, 2013 at 12:54 PM, James Stroud xtald...@gmail.com 
mailto:xtald...@gmail.com wrote:


All that needs to happen is that the community agree on

1. What is the finite set of essential/useful attributes of
macromolecular structural data.
2. What is the syntax of (a) accessing and (b) modifying those
attributes.
3. What is the syntax of selecting subsets of structural data
based on those attributes.

The resulting syntax (i.e. language) itself should be terse, easy
to learn, easy to use, and preferably easy to implement.


Ah, but the nice thing about mmCIF is that it isn't truly finite - 
the PDB may limit what tags are actually included in the distributed 
files, but there is nothing preventing other developers from including 
their own tags, and there is a community process for extending the 
officially defined tags.  Item (2) is very well-established, unlike 
the current chaos of REMARK records.  I think (3) will be left to the 
various libraries to deal with.


-Nat



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Why MAD didn't work but SAD works well

[George Sheldrick]

Dear Yafang,

If radiation damage is not a major problem, MAD should give you more 
phase information than SAD, i.e. better maps, especially
at low resolution. If SAD works but MAD doesn't, there are several 
possible explanations:


1. (most likely) your datasets are inconsistently indexed. This can 
hapen in various ways depending on the Laue group and the unit-cell. If 
you are using hkl2map the plots of the anomalous CC between the 
different datasets are a good quick check. Some programs (e.g. the 
current shelxc) will try to detect this and correct it automatically.


2. You have mixed up the wavelengths or labels of the datasets and so 
the dispersive difference comes out with the wrong sign.


3. You have significant radiation damage and the RIP and dispersive 
differences have opposite signs. Always measure the inflection

dataset last so that they reinforce each other rather than canceling.

4. You have severe radiation damage and only the first (peak) dataset is 
usable.


Best wishes, George


On 08/20/2013 11:05 PM, Yafang Chen wrote:

Hi All,

I have three datasets of SeMet-incorporated protein at peak, infl and 
high wavelength respectively. SAD with peak dataset works well to 
solve the phase problem. However, MAD with all three datasets didn't 
work at all. The completeness of all three datasets are more than 99%. 
So I think radiation damage should not be a problem. Does anyone have 
any idea about the possible reasons that MAD didn't work in this case? 
Thank you so much for any of your help!


Best,
Yafang

--
Yafang Chen
Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] shelx anamalous data

[George Sheldrick]

I'm not sure why you want to do that. If you wish to look at a map or 
poly-Ala trace from SHELXE, just read the .pdb and then .phs files into 
Coot directly. If you want to use them to make pictures with PYMOL, use 
Tim Gruene's SHELX2map. For further information please go to the SHELX 
homepage (Google knows where it is).


George

On 11/14/2013 10:09 PM, Yarrow Madrona wrote:

I'm sorry,

I have not used shelx before and didn't realize in my last post that the
anamolous data is kept separate. I am planning on converting both the
mysad.phs and mysad.pha to mtz files and then merge them. However, I am
not sure of the column lables in mysad.pha. Does anyone know how to get
this info?

-Yarrow




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

[ccp4bb] Fwd: Re: [ccp4bb] shelx anamalous data

[George Sheldrick]

*Dear Eleanor,

There is a reason why I do not provide a routine to go from the .phs
from shelxe to .mtz. If he uses the 'free lunch' option
in shelxe he may finish up refining against the free lunch structure
factors. According to one user who managed to do this
by accident, this gives excellent maps!

Best wishes, George
*


On 11/16/2013 11:16 AM, Eleanor Dodson wrote:

 It is easy enough if you still ant to do it.

 I would feed both into f2mtz separately to make a mysadIplus.mtz and a 
mysadImin.mtz
 then use CAD to combine and change the default labels to something like I(+) 
SIGI(+) and I(-) SIGI(-)

 But as George says Why do you want it? That will change the way you proceed.

 Eleanor
 On 14 Nov 2013, at 21:08, George Sheldrick wrote:


 I'm not sure why you want to do that. If you wish to look at a map or poly-Ala 
trace from SHELXE, just read the .pdb and then .phs files into Coot directly. 
If you want to use them to make pictures with PYMOL, use Tim Gruene's 
SHELX2map. For further information please go to the SHELX homepage (Google 
knows where it is).

 George

 On 11/14/2013 10:09 PM, Yarrow Madrona wrote:

 I'm sorry,

 I have not used shelx before and didn't realize in my last post that the
 anamolous data is kept separate. I am planning on converting both the
 mysad.phs and mysad.pha to mtz files and then merge them. However, I am
 not sure of the column lables in mysad.pha. Does anyone know how to get
 this info?

 -Yarrow



 -- 
 Prof. George M. Sheldrick FRS

 Dept. Structural Chemistry,
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-33021 or -33068
 Fax. +49-551-39-22582



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor

[George Sheldrick]

Adapting programs to make optimal use of modern multicore chips is 
non-trivial and depends very much on the algorithms employed,
there is no magic bullet. First one needs to understand Amdahl's law. 
Assume we have a chip with four cores such as the widely used
Intel i7, amd the program consists of two parts that would each take one 
minute on a single core machine, i.e. the total time taken is 2
minutes. If we succeed in making part 1 fully parallel and part2 is not 
parallel, then the time required will be 0.25+1.0 minutes = 1.25
minutes. However many cores we have, we will never reduce the total time 
to less than 1 minute!. So it is important to make ALL rate

determining stages parallel.

However this is only approximately what happens, because:

1) the i7 uses hyperthreading, so it can run 2 threads on each core. 
However they share the number crunching unit, so this only helps
if the threads frequently have to wait, e.g. to get data from the hard 
disk. For efficient number crunching code the hyperthreading

does not help much.

2) The i7 actually increases its clock frequency if it is running only 
one thread, because the critical factor is the amount of heat
generated. So the speed-up when using multiple cores is smaller than one 
would expect.


3) In special cases (which I have never managed to achieve) the computer 
goes 'super-scalar'. This is because each core has its
own cache memory, so by dividing up a large matrix (too big for one 
cache) so that it is all held in cache, the speedup can be more
than expected for the number of cores, because cache access is much 
faster than RAM.


The key to writing efficient parallel code is to reduce the 
communication between threads to an absolute minimum. By doing this in
the program shelxd (heavy atom location for experimental phasing) I was 
able to achieve a 27 times speedup on a 32 core machine.
However for my other openmp programs the gain was much more modest. For 
some of them there is little advantage in using more

than about 4 cores, primarily because of Amdahl's law.

George


On 12/18/2013 07:50 PM, Marcin Wojdyr wrote:

On Tue, Dec 17, 2013 at 03:32:52PM +, Adam Ralph wrote:

Dear Chang,

 Some CCP4 progs can be used with a multi-core machine,
using OpenMP threads (including refmac it would appear). You will

I think only phaser and aimless.
Of course using 4 cores doesn't mean running 4 times faster
(it's more like ~2x faster for Phaser).


need to compile the code from source rather than taking the binary
versions

These programs are already compiled with openMP in CCP4


 Even if the CCP4 apps are not parallel themselves, they can access
a parallel version of libraries e.g. FFTW, LAPACK. Again you will
probably need to compile CCP4 from source and link with the correct
libraries.

It's possible, but I doubt it it will make noticeable difference.
Refmac runs don't spend much time in LAPACK. Probably the same with
FFTW which is used by programs that use Kevin's clipper.

One thing that can make a big difference is env. variable
GFORTRAN_UNBUFFERED_ALL. It shouldn't be set. If it is set, some
programs run a few times slower.

Marcin



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Sister CCPs

[George Sheldrick]

It would be so nice to have a 'sister CCP' for questions aboud wet-lab 
problems that have nothing to do with CCP4 or crystallographic computing,
The is clearly a big need for it, and those of us who try to keep out of 
wet-labs would not have to wade though it all.


George


On 02/12/2014 03:05 PM, Martyn Winn wrote:

As advertised at the Study Weekend, CCPBioSim is the sister CCP in biomolecular 
simulation. The annual conference will take place in Edinburgh in May, see 
details below.

Cheers
Martyn





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Sister CCPs

[George Sheldrick]

I think that more people read wikis than contribute to them, so this 
'experiment' (see below) is
a little biased. On the other hand, it is often easier to put a question 
to CCP4bb than to search
for the answer in wikis and other documentation, however well organized 
they are.


Kay: can you see how often your XDS wiki (for example) is accessed?

The small number of different contributors to a wiki is however a 
problem. Replying to an email
is something that has to be done almost immediately and reaches 
instantly a large audience.
Making a contribution to a wiki lacks the urgency and can be put off for 
a few weeks, and does
not reward the contributor with immediate feedback or lead to 
controversial discussions.


Perhaps someone should make a list of the questions most frequently 
asked on CCP4bb and
the most helpful replies that they generated. This could even be made 
into a wiki.


George


On 02/14/2014 09:15 AM, Frank von Delft wrote:
Seems it's worth thinking about this as an experiment that has 
actually been done:   BB and wiki have been available in parallel for 
many years now;  so where has all the activity happened, where do 
people go for information - and more to the point, where are other 
people happy to volunteer information?


According to what you say, the experiment has a clear outcome.

Even crystallographers are social beings, and thrive on interaction.  
Wikis don't interact.


I should add I'm not at all clear what problem is being addressed 
here:  if I get an email I don't want to read, I make a tiny 
hand-movement (= hit delete) and it vanishes forever.  Are people 
suggesting we abandon an empirically proven mechanism merely to save 
me the need for this tiny hand-movement?


phx



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

[ccp4bb] Biophysics faculty position at Milwaukee

[George Sheldrick]

Abbas Ourmazd who is physics professor at Milwaukee has asked me to post 
this job advert on CCP4bb:

http://jobs.sciencecareers.org/job/325225/assistant-or-associate-professor-in-biophysics/

George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] small molecule crystallography

[George Sheldrick]

Indexing involves storing all the reflection positions in orthogonal 
reciprocal space and then finding a reciprocal lattice that fits most of 
them.
For a 10 degree frame all we know is that a reflection lies somewhere on 
a sort of 10 degree arc; only two of the three coordinates are
precisely known, which makes indexing difficult. For 0.1 degree frames 
all three coordinates of each reflection are known. For the
purpose of indexing, the number of reflections per frame is irrelevant. 
Unless one is using a detector like an image plate with a long
read-out time, there is no advantage in using frames significantly wider 
than the reflections, they also have a higher background noise level.
This applies equally for small molecules and macromolecules, though for 
a strongly diffracting small molecule a higher background can be

tolerated.

George

On 03/25/2014 09:55 AM, Tim Gruene wrote:

Dear Felix,

as far as I understand we are talking about the frame width, not the
total data range for indexing (10 degree rotations to get enough spots
per frame). I have used 180degrees of data for indexing. At least XDS
places the reflection at the centre of the frame so that with a 10deg
frame width the position is know within +/-5 degree - it is not
surprising indexing fails here.

Regards,
Tim

On 03/25/2014 09:41 AM, Felix Frolow wrote:

Dear Tim,
I am sure your statement is too general and is not very precise.
10 deg oscillation range is as precise as 0.1 deg.  Positions of diffraction 
spots on the area detector have
defined position on rotation axis within the precision/accuracy of the stepping 
motor and the spacial resolution of the area detector
and NOT defined by  oscillation range. If it does, change your setup. We need 
sometimes 10 deg to have enough reflections for indexing. Obviously we
need some reflections to define the orientational matrix and cell dimensions.

FF

Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Mar 25, 2014, at 10:26 , Tim Gruenet...@shelx.uni-ac.gwdg.de  wrote:


Dear David,

I dare claim that rather you do not know how to use the listed programs
in the case for small molecule data rather than none of them were
optimised. E.g. 10degree frames loose all the possible accuracy in the
phi-direction so I am not surprised you had trouble indexing. There is
no reason for that, if you know which parameters to modify.

In addition to that, concluding from one single data set that programs
are not optimised may be a little overinterpreted. In my experience,
this interpretation does not hold.

Best,
Tim

On 03/24/2014 10:03 PM, David Schuller wrote:

Coincidentally, I just spent my day trying to index a lattice of ~ 10 x
10 x 11 A.

Mounting samples: if the compound is stable, just glue it to the end of
a steel pin. No muss, no fuss.

We had to attenuate our synchrotron beam heavily to make it work; motors
can only turn so fast.

We did 10 degree rotations to get enough spots per frame per imaging.
Detector setup allowed for ~ 1 A resolution.

Indexing was a challenge for many of the samples, heavily overloaded
spots and streaks seemed to be causing the most problems.

We tried various of the usual macromolecular programs for indexing;
HKL2000, iMosFlm, XDS, DPS. None of them seem to be optimised for this,
but some of them actually worked in some instances.





On 03/24/14 14:04, Andreas Förster wrote:

Dear all,

I've been approached by a materials student with a petri dish full of
big, sturdy, salty, yellow crystals.  He claims I have the best kit
for single-crystal diffraction on campus.

I would very much appreciate advice on how to deal with this, anything
in the range from won't work to use software X to analyze data in
space group P-43N would be welcome.

Thanks.


Andreas







--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] difference between polar angle and eulerian angle

[George Sheldrick]

There are good arguiments for using quaternions rather than Eulerian  
(or other) angles anyway, this is very well explained in the paper
*Quaternions *in *molecular modeling* 
http://scholar.google.de/scholar_url?hl=enq=http://arxiv.org/pdf/physics/0506177sa=Xscisig=AAGBfm13yuMgR9JJ3LvihnDJIoFFejNTrgoi=scholarrei=Zzs3U__QEYKw7AaL4IDYAwved=0CCoQgAMoADAA' 
by Karney.


George


On 03/29/2014 10:22 PM, Edward Berry wrote:

Thanks, Ian!
I agree it may have to do with being used to computer graphics, where 
x,y,z are fixed and the coordinates rotate. But it still doesn't make 
sense:


If the axes rotate along with the molecule, in the catenated operators 
of the polar angles, after the first two operators the z axis would 
still be passing through the molecule in the same way it did 
originally, so rotation about z in the third step would have the same 
effect as rotating about z in the original orientation.
Or in eulerian angles, if the axes rotate along with the molecule at 
each step, the z axis in the third step passes through the molecule in 
the same way it did in the first step, so alpha and gamma would have 
the same effect and be additive.  In other words if the axes we are 
rotating about rotate themselves in lock step with the molecule, we 
can never rotate about any molecular axes except those that were 
originally along x, y, and z (because they will always be alng x,y,z) 
(I mean using simple rotations about principle axes: cos sin -sin cos).
Maybe I need to think about the concept of molecular axes as opposed 
to lab axes. The lab axes are defined relative to the world and never 
change. The molecular axis is defined by how the lab axis passes 
through the molecule, and changes as the molecule rotates relative to 
the lab axis.  But then the molecular axis seems redundant, since I 
can understand the operator fine just in terms of the rotating 
coordinates and the fixed lab axes. Except the desired rotation axis 
of the polar angles would be a molecular axis, since it is defined by 
a line through the atoms that we want to rotate about. So it rotates 
along with the coordinates during the first two operations, which 
align it with the old lab Z axis (which is the new molecular z axis?) 
. . .   You see my confusion.
Or think about the math one step at a time, and suppose we look at the 
coordinates after each step with a graphics program keeping the x axis 
horizontal, y axis vertical, and z axis coming out of the plane. For 
Eulerian angles, the first rotation will be about Z. This will leave 
the z coordinate of each atom unchanged and change the x,y 
coordinates.  If we give the new coordnates to the graphics program, 
it will display the atoms rotated in the plane of the screen (about 
the z axis perpendicular to the screen).  The next rotation will be 
about y, will leave the y coordinates unchanged, and we see rotation 
about the vertical axis. Final rotation about z is in the plane of the 
screen again, although this represents rotation about a different axis 
of the molecule.  My view would be to say the first and final rotation 
are rotating about the perpendicular to the screen which we have kept 
equal to the z axis, and it is the same z axis.


Ed

 Ian Tickle 03/29/14 1:39 PM 
Hi Edward

As far as Eulerian rotations go, in the 'Crowther' description the 2nd 
rotation can occur either about the new (rotated) Y axis or about the 
old (unrotated) Y axis, and similarly for the 3rd rotation about the 
new or old Z.  Obviously the same thing applies to polar angles since 
they can also be described in terms of a concatenation of rotations (5 
instead of 3).  So in the 'new' description the rotation axes do 
change: they are rotating with the molecule.


For reasons I find hard to fathom virtually all program documentation 
seems to describe it in terms of rotations about already-rotated 
angles.  If as you say you find this confusing then you are not 
alone!  However it's very easy to change from a description involving 
'new' axes to one involving 'old' axes: you just reverse the order of 
the angles.  So in the Eulerian case a rotation of alpha around Z, 
then beta around new Y, then gamma around new Z (i.e. 'Crowther' 
convention) is completely equivalent to a rotation of gamma around Z, 
then beta around _old_ Y, then alpha around _old_ Z.


So if you're used to computer graphics where the molecules rotate 
around the fixed screen axes (rotation around the rotating molecular 
axes would be very confusing!) then it seems to me that the 'old' 
description is much more intuitive.


Cheers

-- Ian


On 27 March 2014 22:18, Edward A. Berry ber...@upstate.edu 
mailto:ber...@upstate.edu wrote:


According to the html-side the 'visualisation' includes two
back-rotations in addition to what you copied here, so
there is at
least one difference to the visualisation of the Eulerian
angles.


Right- it says:
This can also be 

Re: [ccp4bb] SAD Pattersons (previously space group problem)

[George Sheldrick]

Dear Chen,

If you don't know how many sites to expect - and in some cases, e.g. an 
iodide soak, this is inevitable - I recommend trying different numbers 
(FIND N in shelxd)  and choosing the one where the occupancy of peak N 
comes out as about 0.2. If it is higher you need a higher N and vice 
versa. hkl2map makes a nice plot of the occupancies but you can also 
simply look at the values in the .res file. You have to be careful with 
sites on special positions because the occupancy is divided by the 
multiplicity of the position. Except for some soaks, it is unlikely that 
there will be an atom on a special position so it is recommended that 
the second MIND parameter is set to say 2.2 (the default) to reject 
peaks on special positions. In borderline cases you will also have to 
try different resolutions for truncating the anomalous data (e.g. SHEL 
99 2.0), but if you are looking for disulfide sulfurs you may also need 
to search for M disulfides in the peaksearch (DSUL M and MIND 3.5) 
because if the resolution cut is higher than 2A the individual sulfurs 
may not be resolved.


The current shelxe allows you to refine the heavy atoms before doing 
density modification (-zN for a maximum of N sites. for SAD you should 
also specify -h unless you are using a separate higher resolution native 
dataset). This should always be used except when you had to use DSUL in 
shelxd, because shelxe does not (yet) know about disulfides.


Heavy atom Pattersons are inevitably noisy, especially for weak SAD 
data, both because of the low I/sigma of the anomalous differences and 
because we are using the anomalous difference as an approximation to the 
true heavy atom structure factor. Pattersons calculated from MAD FA 
values do not suffer from this approximation but may be affected more by 
radiation damage. The Patterson is still useful to see if any heavy 
atoms are present, but the above trial and error method is a better way 
of determining the number of heavy atoms. This also explains why some 
Patterson density may be negative, especially close to stronger positive 
peaks, other reasons in the case of SAD are the missing reflections in 
centrosymmetric projections and possible  incomplete coverage of Friedel 
pairs.


Best wishes, George



On 04/02/2014 04:16 AM, Chen Zhao wrote:
By the way, I have another question related to the number of sites. I 
just rethought about what Herman mentioned, and I just realized that 
the number of sites, at least strong sites, could be guessed from an 
anomalous Patterson map. Therefore I looked at the anomalous Patterson 
of my data. The map indicates that the signal is very weak, and there 
are only 4 non-origin positive peaks (3 effective peaks, because 2 are 
symmetry equivalent), indicating there are at most 3 heavy atoms 
(3x2=6) if all of them contribute to the map. However, in shelxd, I 
can get optimal results from 6 sites out of the same data set. I am 
not sure whether this is because the anomalous Patterson is not 
sensitive enough. Now I am more confused about the criteria in 
choosing the parameters when running shelx and all other programs. 
What should be the general practice? Should I rely more on the 
anomalous Patterson or more on the better scores reported? When I 
tried to optimize the results by changing the parameters (either when 
locating sites or when phasing), am I more heading for the real signal 
or more simply tweaking the parameters? Maybe the golden standard 
would be whether you could solve the structure.


Another question is, although from the Euler's equation I could 
understand negative Patterson peaks (maybe I am wrong), I am still not 
clear what negative Patterson peaks represent and why people generally 
don't talk about it. In the specific data I am talking about above, 
there is a negative Patterson peak at the same position as a positive 
Patterson peak with the same height. Is there any indication about this?


Thank you so much for your attention!




On Tue, Apr 1, 2014 at 2:00 PM, Nazia Nasir 
Phd2009,ProteinCrystall.Lab nazia.nasi...@nii.ac.in 
mailto:nazia.nasi...@nii.ac.in wrote:


Dear Jurgen,

The beam position is fine. we have collected many data sets before
and after this data. Moreover, we the Technical scientist always
checks the beam position before we mount the crystals.

Thanks


On Tue, Apr 1, 2014 at 11:23 PM, Jurgen Bosch jbos...@jhu.edu
mailto:jbos...@jhu.edu wrote:

check your beam position
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742 tel:%2B1-410-614-4742
Lab: +1-410-614-4894 tel:%2B1-410-614-4894
Fax: +1-410-955-2926 tel:%2B1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Confusion about space group nomenclature

[George Sheldrick]

In my program documentation I usually call these 65 the Sohnke space 
groups, as defined by the IUCr:

http://reference.iucr.org/dictionary/Sohnke_groups

George


On 05/02/2014 02:35 PM, Jim Pflugrath wrote:
After all this discussion, I think that Bernhard can now lay the claim 
that these 65 space groups should really just be labelled the Rupp 
space groups.  At least it is one word.


Jim


*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 
Bernhard Rupp [hofkristall...@gmail.com]

*Sent:* Friday, May 02, 2014 3:04 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Confusion about space group nomenclature
….

Enough of this thread.

Over and out, BR




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] correct pdb encoding for split-personality solvent HETATM?

[George Sheldrick]

Dear Alastair,

As you point out, SHELXL allows atom names, RESIdue numbers and PARTs 
(=Altlocs) to be used in any combination. The only rule is that no two 
non-hydrogen atoms may have the same settings for all three. Other 
refinement programs may be more restrictive.


Best wishes, George


On 05/14/2014 08:26 PM, Alastair Fyfe wrote:
thanks Tim. I have been using different AltLoc values (A,B) and 
different  Atom name values (HOH,CA) but the problem seems to be 
which value to set  for the  Residue name field. Assigning different 
residues numbers would seem to lose the distinction between partial 
and alternate  occupancy. The ins file seems to have no problem with 
the pattern

RESI CA
PART 1
CA ..
PART 2
O ..
PART 0



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] refine an ion atom with different status

[George Sheldrick]

I agree with Pavel. Even for accurate small molecule data with R-values 
below 3% the differences are hardly significant, the 'B-factors' 
compensate so well. The large majority of small molecule structures are 
refined with neutral atom scattering factors even if ions are present. 
The calculated scattering factor for an isolated ion in the gas phase is 
not really appropriate for the environement of an ion in the crystal 
anyway.


George


On 06/20/2014 07:18 AM, Pavel Afonine wrote:

Hi Bernhard,

phenix.refine makes use of charge if specified in PDB file (rightmost 
column after the chemical element type) to use appropriate 
form-factors. However, occupancies and B-factors are very efficient 
mops to accommodate a broad range of discrepancies between model and 
reality. So whether the effect of using charge is going to be 
noticeable, I guess, depends on the data quality (resolution, 
completeness, etc) and how strong the effect itself is.


Also, it should be relatively easy to make a numerical experiment with 
calculated data to see how the total scattering brakes down into 
individual contributions.


Pavel


On Thu, Jun 19, 2014 at 6:42 PM, Bernhard Rupp 
hofkristall...@gmail.com mailto:hofkristall...@gmail.com wrote:


“.. change the valence of ion or metal except by changing the
occupancy”

Changing the occupancy is entirely different from changing
valence. The former scales the scattering function proportionally,
while the elimination of outer shell electrons predominantly
reduces the very low resolution part (starting at f000) of the
scattering function. Verifying the correct scattering function
(e.g. Fe+++ vs Fe++ vs Fe atomic) used by the refinement program
could be useful. I am curious: Garib, Pavel, Busters: How is that
currently implemented?

Best, BR

*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Wang, Bing
*Sent:* Thursday, June 19, 2014 10:44 PM
*To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] refine an ion atom with different status

Hi CCP4 guys,

I have a structure with heme containing an ion atom in it. Except
the 4 coordinated nitrogen atoms in the heme, this ion also
coordinates with one histidine residue and one ligand. But I found
two negative red balls (top one and bottom one) around the ion,
which is perpendicular to the heme plate and keeping in the same
line with the histidine and my ligand (See the figure Ion_100 from
coot in the attachment). I guess this ion has different status in
it (e. g. mixture of Fe2+ and Fe3+). I simply tried the lower
occupancy of ion. It clearly eliminate the negative ball at the
bottom and most of the negative balls at the top, but also
produced one more positive peak with slight movement instead of
the negative ball at the bottom (See the figures Ion_90, Ion_85,
Ion_80). The numbers in the image name represents the different
occupancy (100 means 100%, 80 means 80%).

So any suggestions to solve this problem? Except changing the
occupancy, is there a more precise way to change the valence of
ion or metal in coot, and then refine in Refmac or Phenix?

Thanks!

Bing





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

[ccp4bb] Fwd: Re: [ccp4bb] Shelxc failure

[George Sheldrick]

Dear Roberto,

If you are using shelxc/d/e, it is best to read the XDS.ASCII.HKL file 
DIRECTLY into shelxc. This is what hkl2map does.


When you run shelxe (from the command line or hkl2map), you usually need 
to try both hands of the heavy atom substructure. If the 'contrast' for 
one hand is significantly better than for the other, then it is the 
solution. Sometimes (e.g. because the heavy atom substructure is 
centrosymmetric, e.g. one heavy atom in a polar space group) both 
solutions have the same contrast and both are correct. However the 
poly-Ala trace in shelxe will only work for the correct hand because 
proteins are chiral. A particularly useful check is the CC against the 
native data for the poly-Ala trace, if it is higher than 25% you have 
solved the structure. This also applies when shelxe is used to expand 
from a poor MR solution.


The phases from shelxe are already density modified, it is NOT a good 
idea to density modify them again. You should simply read the .pdb and 
then the .phs files from shelxe into Coot and look at the map yourself. 
If it makes sense then you can either dock the side-chains yourself 
using the facilities in Coot, or use Buccaneer to do this automatically.


shelxe does however currently require native data to relatively high 
resolution (at least 3A and better 2A).


Best wishes, George


On 06/20/2014 05:54 PM, Roberto Valverde wrote:

Hi CCP4BB,

First time posting here, greetings!

I have two questions:

Question 1:
I am trying to use Shelx C/D/E pipeline to solve single anomalous 
data.  I processed the data in XDS, and scaled the data in aimless.  
When I run shelx c/d/e pipeline I encounter this error:


#CCP4I TERMINATION STATUS 0 No ins file from shelxc


I assume this means there is no instruction file.  How do define an 
instruction file?


Question 2:
As an alternative I obtained phases from hkl2map, and wanted to 
perform density modification using Parrot.  I used the ha.pdb file I 
obtained from hkl2map to define the atom sites.  The program finished 
and produced two possible solutions.  Both maps look terrible, far 
worse than the map hkl2map produced.  What am I doing wrong?


Thank you,
Roberto




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] [phenixbb] So what is unique?

[George Sheldrick]

I think that 'observed' goes back to whether it was possible to see a 
reflection (and estimate its intensity by eye) on the photographic FILM. 
In small molecule crystallography it is usually understood to mean 
F4sigma(F) (or I2sigma(I)).


George


On 07/15/2014 07:02 PM, Edward A. Berry wrote:

So on second thought, practically speaking I guess observed is all,
since we never see the ones that are rejected by the -3 sigma
observed criterion

On 07/15/2014 12:44 PM, Edward A. Berry wrote:

I don't think observed means all the reflections that were integrated,
becasue one of the other parameters is the criterion for a reflection
to be considered observed, so that observed is a subset of all.
Here are some lines I saved from an adit2 session (some years back,
but I believe it was the same in a recent deposition)
I don't think the questions fit very well the way we collect and
process data today, but I think most of these are optional.
What I called Rsym should probably be called Rmerge,
from merging frames not merging crystals.

Observed criterion sigma(F)  null 
Observed criterion sigma(I) -3
Resolution (high) 3.000
Resolution (low) 42.68
Number unique reflections (all)  ? 
Number unique reflections (observed) 141782
Percent possible (observed) 91.8
R-merge I (observed) ?
R-sym I (observed) 0.124

On 07/15/2014 11:26 AM, Kenneth A. Satyshur wrote:
There is some disagreement on terms used to deposit data. We need a 
definition and an algorithm

for each definition.

Unique Reflections

My definition is all the possible reflections out to the highest 
resolution reported not related by symmetry.
  Where can I find this? The .mtz contains a list of all HKL 
calculated to the highest resolution. Usually, we
are not able to measure all these diffraction spots due to limits of 
the detector, mechanical limits, crystal

orientation, etc.

'Total reflections'
The depositions server asks for total reflections. I assume it wants 
only those unique reflections we were able to
collect, regardless of the sigma cut off. These are called 
'observed'. The total we use in refinement will be a subset
of the 'unique observed' that are cut on sigma. However, some 
crystallographers believe that we should not cut
on sigma since some of the intensities may in fact be zero. Is this 
a question for the Refmac and Phenix people?


Please give us some guidance and maybe a reference or two that we 
can use.

thanks

--
Kenneth A. Satyshur, M.S.,Ph.D.
Senior Scientist
University of Wisconsin
Madison, Wisconsin 53706
608-215-5207



___
phenixbb mailing list
pheni...@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb








--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] aimless and anisotropic scaling (and the docs?)

[George Sheldrick]

I think that anything that irrevocably modifies the experimental data 
should be avoided whenever possible. Since anisotropic scaling is a 
relatively fast calculation and there are several ways of doing it, it 
is better to apply it locally when it is needed, e.g. in phasing (where 
it is applied by phaser and shelxe etc.) and refinement (with refmac or 
phenix_refine etc.). Provided that the standard deviations of the 
observed intensities are properly taken into account, anisotropic data 
truncation is not so important (i.e. as usual I agree with Garib and Phil).


George

On 04/25/2012 06:19 PM, Phil Evans wrote:

You can get the aimless documentation from

ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html

pending its official release through CCP4

No it does not do anisotropic scaling as such. That needs some sort of model of the 
ideal intensity, probably best calculated from a model

I'm not sure that anisotropic cutoffs are a good idea. I believe Garib thinks 
they are not and I generally defer to him

Phil

On 25 Apr 2012, at 17:00, Bryan Lepore wrote:


wondering if aimless performs anisotropic scaling or elliptical
rejections lately.

I ask because:

[1] last I knew, scala did not
[2] I can't seem to google up the aimless manual as readily as scala

... also, what consesquence would mosflm anisotropic resolution limits
have on scaling (if aimless anisoscaling were true).

-Bryan



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] ShelXL and Coot

[George Sheldrick]

You probably need to insert the space group name into the CRYST1 record. 
Tthe version of SHELXL that I am planning to release this summer already 
deduces the space group name from the LATT and SYMM cards and puts it 
there. If you read the .res file into Coot instead of the .pdb, Coot can 
deduce the space group automatically. You can then read in the .fcf file 
(created with LIST 6) so that Coot can generate the maps. However if you 
use Coot to write out the .ins file for the next SHELXL refinement job, 
you may need to do some editing, e.g. change the occupancies of new 
atoms from 1.0 (which shelxl understands as being free to refine) to 
11.0 (which means fix it at 1.0). You may also have to reinstate the 
'free variables' used for occupancies etc., because Coot (Refmac) does 
not (yet) use this very useful concept.


George

On 05/06/2012 12:07 AM, Badsha Mukherjee wrote:

Hi,

I am unable to open the output pdb file from ShelXL in Coot.

Any suggestion will be appreciated.

Thanks in advance

Badsha



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma

[George Sheldrick]

In SHELXL. a refinement program sometimes used by small molecule 
crystallographers, all Fourier map for at least the last 20 years were 
weighted by Ic^2/(Ic^2+sigma^2(I)), where Ic is the calculated squared 
structure factor and sigma(I) is the square root of 1/w. w is the weight 
assigned to a reflection in the refinement (e.g. w=1/(sig(I)^2+(gI)^2), 
where sig(I) is the esd of the measured intensity I and g is a small 
constant. This purely empirical scheme appears to result in a 
significant reduction in the noise level of the map, at least for 
typical small molecule structures. Such schemes have been called 
'maximum likelihood by intuition', a proper maximum likelihood treatment 
taking the esds of the intensities into account would of course do much 
better.


George

On 05/23/2012 06:59 PM, Dale Tronrud wrote:

On 05/23/12 08:06, Nicholas M Glykos wrote:

Hi Ed,



I may be wrong here (and please by all means correct me), but I think
it's not entirely true that experimental errors are not used in modern
map calculation algorithm.  At the very least, the 2mFo-DFc maps are
calibrated to the model error (which can be ideologically seen as the
error of experiment if you include model inaccuracies into that).

This is an amplitude modification. It does not change the fact that the
sigmas are not being used in the inversion procedure [and also does not
change the (non) treatment of missing data]. A more direct and relevant
example to discuss (with respect to Francisco's question) would be the
calculation of a Patterson synthesis (where the phases are known and
fixed).



I have not done extensive (or any for that matter) testing, but my
evidence-devoid gut feeling is that maps not using experimental errors
(which in REFAMC can be done either via gui button or by excluding SIGFP
from LABIN in a script) will for a practicing crystallographer be
essentially indistinguishable.

It seems that although you are not doubting the importance of maximum
likelihood for refinement, you do seem to doubt the importance of closely
related probabilistic methods (such as maximum entropy methods) for map
calculation. I think you can't have it both ways ... :-)




The reason for this is that model errors as estimated by various
maximum likelihood algorithms tend to exceed experimental errors.  It
may be that these estimates are inflated (heretical thought but when you
think about it uniform inflation of the SIGMA_wc may have only
proportional impact on the log-likelihood or even less so when they
correlate with experimental errors).  Or it may be that the experimental
errors are underestimated (another heretical thought).

My experience from comparing conventional (FFT-based) and maximum-entropy-
related maps is that the main source of differences between the two maps
has more to do with missing data (especially low resolution overloaded
reflections) and putative outliers (for difference Patterson maps), but in
certain cases (with very accurate or inaccurate data) standard deviations
do matter.

In a continuation of this torturous diversion from the original question...

Since your concern is not how the sigma(Fo) plays out in refinement but
how uncertainties are dealt with in the map calculation itself (where an
FFT calculates the most probable density values and maximum entropy would
calculate the best, or centroid, density values) I believe the most
relevant measure of the uncertainty of the Fourier coefficients would be
sigma(2mFo-DFc).  This would be estimated from a complex calculation of
sigma(sigmaA), sigma(Fo), sigma(Fc) and sigma(Phic).  I expect that the
contribution of sigma(Fo) would be one of the smallest contributors to this
calculation, as long as Fo is observed.  I wouldn't expect the loss of
sigma(Fo) to be catastrophic.

Wouldn't sigma(sigmaA) be the largest component since sigmaA is a function
of resolution and based only on the test set?

Dale Tronrud




All the best,
Nicholas





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] P321 space group reindex problem

[George Sheldrick]

Which programs require that the data be the 'standard' a.u.? None of 
mine require this.


George

On 05/29/2012 03:44 PM, Ian Tickle wrote:

Mark, thanks for pointing that out, I see it now:

In P321 the only possible alternate indexing is (-h, -k, l): this is a
2-fold || c which is an operator of the hexagonal lattice but is not
an equivalent reflection.

The standard CCP4 a.u. is h = k, l= 0 or h  k, k= 0, so for
example (3,2,1) would be in the standard a.u. (3  2 and 2= 0).  In
the alternate indexing this would be (-3, -2, 1); however it's
impossible to transform this to the a.u. with any non-inverting
equivalent.  The only possibility is to invert the hand, i.e. to (3,
2, -1) which is again in the a.u..

So the required re-indexing operator to match (3, 2, -1) with (3, 2,
1) is (h, k, -l) which reindex won't allow without the LEFT keyword
(and you would be well-advised to avoid doing it with phase columns!).

Cheers

-- Ian


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] High Rfree values and using Bruker detector w/ iMosflm

[George Sheldrick]

Dear Annette,

I suspect that a trivial error like confusing F and intensity is the 
cause of your problem. You would probably get a better response if you 
sent your message to the very informative Bruker mailing list or asked 
one of the Bruker applications scientists. If you wish to send me your 
data in confidence I would be happy to try to sort it out for you. I 
suggest that you send me the .raw files produced by the Bruker 
integration program SAINT after gzipping them, please do not send the 
frames(!). Note that the Bruker control software can also write 
'unwarped' frames if you really need them, however we get excellent data 
with the normal Bruker procedure (SAINT, SADABS, XPREP and then F2mtz 
etc.). As Tim says, XPREP is not an integration program but it does 
determine the space group and provide a lot of useful statistics.


My other strong recommendation, irrespective of which beamline or 
in-house system you are using, is to collect a quick cubic insulin or 
lysozyme dataset from time to time. This will tell you if all the 
hardware and software is functioning correctly, and incidentally 
provides you with a accurate X,Y beam position which can be invaluable 
for indexing problem datasets.


Best wishes, George

On 06/25/2012 06:25 PM, Annette Medina Morales wrote:

Hi,

We collected data using our in-house Bruker Proteum X8 diffractometer 
and after using Xprep to integrate the images the output HKL file was 
converted to an mtz using CCP4's Scalepack2mtz.  The prp file 
generated by Xprep shows good statistics with completeness and good 
data for 2.4 angstrom resolution.  Mean intensity/sigma, Rsym, and 
Rsigma have good values.  Pointless indicates space group is P212121. 
Later we used molecular replacement and obtained a good model and 
Refmac to refine the structure.  The electron density maps show the 
correct density for the amino acids, waters, and other metals in the 
structure and refinement with coot improves the electron density 
around the atoms.


However, after multiple rounds of refinement the R value drops to 0.25 
but Rfree does not go below 0.35!  Also, the structure factors are 
very low.  We have tried all the obvious reasons as not having the 
correct space group which is not the case, and have included NCS 
restraints as well as TLS parameters to improve the refinement.  None 
of this has helped in helping the Rfree value go down. Since we never 
have this problem with data collected from other detectors (like at 
SSRL), and this problem repeats with other datasets from collected 
in-house, we suspect that the original integration of the images using 
Xprep might be a problem and might be doing something to the 
reflection data.  Does anyone have any experience with this?


Also, I have recently tried using iMosflm to refine the data but using 
the .sfrm images from the Bruker detector is problematic since I get 
an Application error that reads invalid command name and an Image 
read error that reads Error reading image header.  Message from 
Mosflm is error reading record 33: check image is correct size.  Does 
anyone have any advice on how to correct this since I understand that 
iMosflm is supposed to be able to read Bruker .sfrm images? Thanks! 
Annette





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] Off-topic: Best Scripting Language

[George Sheldrick]

It is the lack of compatibility between different versions mentioned by 
Ethan that really put me off learning PYTHON. In contrast, the 
FORTRAN-66 program SHELX76 still compiles and runs correctly with any 
modern FORTRAN compiler. The only significant 'new' features that I now 
use are dynamic array allocation (introduced in FORTRAN-90) and OpenMP 
support for multiple CPUs, but even programs using OpenMP would still 
work with older compilers because the OpenMP instructions would be 
treated as comments.


George

On 09/12/2012 08:28 PM, Ethan Merritt wrote:

On Wednesday, September 12, 2012 09:52:09 am Jacob Keller wrote:

For the specific purpose you list -
input from tab-delimited data
output to simple statisitical summaries and (I assume) plots
- it sounds like gnuplot could do the job nicely.


I wasn't aware that gnuplot can do calculations--can it? I was probably
going to use it somewhere as a plotting option.

Here's a simple-minded example using a dump of the current contents
of the PDB from www.pdb.org as a comma-separated file with ~65000 entries.
The input file was previously filtered to contain only X-ray structures
between 1 and 4 Angstroms resolution.

gnuplot  !head -3 PDB.csv
PDB ID,R Observed,R All,R Work,R Free,Refinement Resolution
100D,0.145,,0.145,,1.90
101D,0.163,,,0.252,2.25

gnuplot  set datafile separater ,
gnuplot  set datafile nofpe_trap   # trap handling greatly slows large data 
sets
gnuplot  stats 'PDB.csv' using R Observed prefix Robs

* FILE:
   Records:  63029
   Out of range: 0
   Invalid:  0
   Blank:2
   Data Blocks:  2

* COLUMN:
   Mean:  0.1982
   Std Dev:   0.0334
   Sum:   12494.6900
   Sum Sq.:2547.3068

   Minimum:   0.0450 [24518]
   Maximum:   0.9700 [45024]
   Quartile:  0.1770
   Median:0.1970
   Quartile:  0.2180

gnuplot  print Robs_mean
  0.198237160672072

gnuplot  #calculate correlation of Robs with Resolution
gnuplot  stats 'PDB.cvs' using R Observed:Refinement Resolution  nooutput
gnuplot  print STATS_correlation
  0.595763711910418

I've attached graphical output of the same data following some sorting,
filtered, binning, etc, with output to a PDF file.

You can do all this in R also.   R has a larger collection of statistics 
options,
but is not as good at dealing with really large data sets.  IMHO gnuplot has 
more
flexible options for graphical output.


Otherwise I'd recommend perl, and dis-recommend python.


Why are you dis-ing python? Seems everybody loves it...

I'm sure you can google for many reasons I hate Python lists.

Mine would start
1) sensitive to white space == fail
2) dynamic typing makes it nearly impossible to verify program correctness,
and very hard to debug problems that arise from unexpected input or
a mismatch between caller and callee.
3) the language developers don't care about backward compatibility;
it seems version 2.n+1 always breaks code written for version 2.n,
and let's not even talk about version 3
4) slw unless you use it simply as a wrapper for C++,
in which case why not just use C++ or C to begin with?
5) not thread-safe

 you did ask...

Ethan




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] Off topic

[George Sheldrick]

shelx .hkl files often have a blank line or a line filled out with zeros 
at the end as a terminator. This is useful if you wish to edit in extra 
information such as the cell dimensions after this line, but is not 
obligatory. However if you concatenate the files with cat or a text 
editor you may need to remove such a line from the middle of the 
concatenated file. However as Tim says, you will almost certainly need 
to scale them together, in which case xprep is a good choice. It allows 
you to either merge the intensities and their esds or to scale but not 
merge them. If required you can also use it to add free R flags (or 
transfer them from another file).


George

On 09/15/2012 12:20 PM, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Rex,

if you are talking about shelx hkl-files which contain no extra
information, you can use 'cat', available only probably all unixoidal
operating systems:
cat 1.hkl 2.hkl  3.hkl

It might, however, be more reasonable to scale the two files together.
xprep can do this.

Cheers,
Tim

On 09/15/2012 11:10 AM, Rex Palmer wrote:

Is there an easy way to make two .hkl files into one continuous
file?


Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQVFZsUxlJ7aRr7hoRApyKAKCtVhAaZZCIeomC97Yn0pJ9YberxgCbBE2x
mdSkUO5Yz7URJoUCWEWfF3w=
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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] coot, shelx res files and R32 (H32)

[George Sheldrick]

shelxl-2012 does include the space group in a way that Coot understands 
when it writes a .pdb file. This version is in the final beta-testing 
stage with a lot of new features (mainly for small molecules) and no 
known bugs, so I hope to release it soon. If anyone would like to try it 
now please send me an email.


George

On 11/19/2012 02:13 PM, Petr Leiman wrote:

Dear Developers of Coot,

I believe that coot has never been able to display the crystallographic 
symmetry of a R32:H shelxl .res file. As a result, water picking does not work 
properly for such a file. Everything else seems to work fine. This is not a 
huge problem, but it would be nice to be able to see symmetry atoms without 
loading the corresponding shelxl .pdb (which accidentally lacks the space group 
information anyway, so it has to be edited prior to loading). Again, not a big 
problem but I believe it is an easy fix in the code, so hopefully this will be 
done at some point in the future.

Thank you,

Petr


Petr Leiman
EPFL
BSP-415
CH-1015 Lausanne
Switzerland




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] The information of shelxc_fa.lst

[George Sheldrick]

That is a list of the strongest Patterson peaks, the ones marked with 
'*' are used
as translation search vectors to kick-start the heavy atom location. 
x,y,z are the
crystal coordinates of the peaks, height is the peak height, mult 
indicates how the
peaks have coalesced because they are on special positions (in Patterson 
space)
and length is the distance of the peak from the origin, i.e. the vector 
length.


George

On 11/30/2012 09:54 AM, Wei Feng wrote:

Dear all,
When I used shelxc/d/e to locate the Se atoms in a protein, I found an 
output file shelxc_fa.lst.
Does anyone can tell me the meaning of the indicates in shelxc_fa.lst 
(red word):

Thanks a lot!
Ding wei

shelxc_fa.lst:
Patterson (* indicates vector selected for search)

X Y Z Height Mult Length

0. 0. 0. 999.9 0.0435 0.00
0.0553 0.0553 0.0159 43.8 0.5000 5.22
0.5511 0. 0.5000 33.8 0.2500 99.53
0.9102 0.8730 0.0163 31.7 1. 9.29 *






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] Fwd: Re: [ccp4bb] The information of shelxc_fa.lst

[George Sheldrick]

Dear Ding Wei,

The Patterson function is discussed in most crystallographic text books. 
I recommend the IUCr text by Giacovazzo et al., Fundamentals of 
Crystallography starting about page 423 in the third edition for a 
detailed discussion. If you just require a sorted peak list, shelxd is 
as good as any and you clearly already know how to use it. The older 
shelxs has further Patterson options, as do many other programs such as 
the CCP4 program FFT.


Best wishes, George

On 12/07/2012 11:31 AM, ccp4...@hotmail.com wrote:

Dear professor George Sheldrick,
I am sorry to bother you again!
I read that letter some days ago. And now I also want to know which 
formula or soft can be used to calculate the patterson peaks from 
sca/mtz file.

Thank you for your time!
Ding wei


At 2012-12-07 18:08:20,George Sheldrick 
gshe...@shelx.uni-ac.gwdg.de wrote:


I already replied to your email on CCP4bb! Here is a copy:

 Original Message 
Subject:Re: [ccp4bb] The information of shelxc_fa.lst
Date:   Fri, 30 Nov 2012 10:32:50 +0100
From:   George Sheldrick gshe...@shelx.uni-ac.gwdg.de
CC: CCP4BB@JISCMAIL.AC.UK



That is a list of the strongest Patterson peaks, the ones marked
with '*' are used
as translation search vectors to kick-start the heavy atom
location. x,y,z are the
crystal coordinates of the peaks, height is the peak height, mult
indicates how the
peaks have coalesced because they are on special positions (in
Patterson space)
and length is the distance of the peak from the origin, i.e. the
vector length.

George

On 11/30/2012 09:54 AM, Wei Feng wrote:

Dear all,
When I used shelxc/d/e to locate the Se atoms in a protein, I
found an output file shelxc_fa.lst.
Does anyone can tell me the meaning of the indicates in
shelxc_fa.lst (red word):
Thanks a lot!
Ding wei

shelxc_fa.lst:
Patterson (* indicates vector selected for search)

X Y Z Height Mult Length

0. 0. 0. 999.9 0.0435 0.00
0.0553 0.0553 0.0159 43.8 0.5000 5.22
0.5511 0. 0.5000 33.8 0.2500 99.53
0.9102 0.8730 0.0163 31.7 1. 9.29 *






-- 
Prof. George M. Sheldrick FRS

Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582







--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] archival memory?

[George Sheldrick]

Punched cards, stored in a sealed dry box, and perhaps irradiated to 
kill off any bacteria, should long outlive any magnetic or capacitive 
storage medium. If it is difficult to find a working card reader, they 
could always be read by eye, though that might be tedious. Their EBCDIC 
code is not ASCII, but at least it is well documented.

George


On 12/12/2012 11:35 PM, Artem Evdokimov wrote:
Given that it's basically a solid state tiny capacitor, temperature 
should indeed be a huge factor :) I am actually considering storing 
some flash sticks in a freezer, to see what happens. And in LN2 as well...

Artem

On Wed, Dec 12, 2012 at 4:14 PM, Richard Gillilan r...@cornell.edu 
mailto:r...@cornell.edu wrote:


I don't think memory sticks have any internal electrolytics or
power supplies. Both USB and FAT32 are widely documented standards
in this era, so while they might no longer be supported (FAT32 is
already very old), information on how to communicate and decode
data will still likely be available. RS232, for example, is now 50
years old and one can still find adapters and software.

Richard

On Dec 12, 2012, at 4:45 PM, Roger Rowlett wrote:


Maybe the memory chips will retain their bits for 100 years, but
what about the driver hardware or internal power supply? Anyone
had an electrolytic capacitor last for 100 years? Just sayin...

I like the image of the USB sticks in the -80 freezer, though. :)
___
Roger S. Rowlett
Gordon  Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245 tel:%28315%29-228-7245
ofc: (315)-228-7395 tel:%28315%29-228-7395
fax: (315)-228-7935 tel:%28315%29-228-7935
email: rrowl...@colgate.edu mailto:rrowl...@colgate.edu


On 12/12/2012 4:38 PM, Artem Evdokimov wrote:

Or... (gasp) store a regular USB drive in a freezer, yes? If the
relationship between data decay rate and temperature indeed
follows the same good old Arrhenius formula then any old USB
drive is virtually endless at -80C and safe for human life span
at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your
USB in some ice packs so defrost doesn't kill it).
If this works, feel free to send me money, SanDisk...
Artem

On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan
r...@cornell.edu mailto:r...@cornell.edu wrote:

SanDisk advertises a Memory Vault disk for archival
storage of photos that they claim will last 100 years.

(note: they do have a scheme for estimating lifetime of the
memory, Arrhenius Equation ... interesting. Check it out:
www.sandisk.com/products/usb/memory-vault/
http://www.sandisk.com/products/usb/memory-vault/ and
click the Chronolock tab.).

Has anyone here looked into this or seen similar products?

Richard Gillilan
MacCHESS










--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] 3D alignment of points (atoms)

[George Sheldrick]

A computationally elegant and probably faster approach is to use 
quaternions, proposed by MacKay in Acta Cryst. A40 165-166. For a recent 
description of this method see 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958452/


George

On 12/27/2012 09:09 PM, Dale Tronrud wrote:

If you just want the mathematics and are willing to roll your own
code, you can use the method of Wolfgang Kabsch.  I see this has been
enshrined in a Wikipedia page at

http://en.wikipedia.org/wiki/Kabsch_algorithm

This is what I've used when I've wanted to superimpose points where
the mapping between the points is defined.  If the points in your
tetramer aren't pathological, like lying in a common plane, you
shouldn't have to worry about SVD and can just perform the matrix
inversion.

Dale Tronrud


On 12/27/12 11:16, Waugh, David (NIH/NCI) [E] wrote:

Greetings,

I have what seems like a relatively simple problem to solve, but have not been 
able to do so using the software tools I know about. I have two sets of 4 
points in 3D space (atoms in PDB files). They represent equivalent positions in 
two tetrameric proteins. I would like to align these points in one PyMol or 
Coot file. I don’t want a NEW set of points representing the LSQ average of the 
two sets, which is what I get in Coot’s SuperPose. Instead I am looking for a 
way to “superimpose” one atom from each set and then rotate one set for the 
best fit. I’m not an intuitive expert on symmetry, but I think there is 
probably only one best solution to this problem, right? I also need the atomic 
distances to be on the same scale in the two sets of points.

Thanks for any help!

Dave Waugh

--
David S. Waugh, Ph.D.
Macromolecular Crystallography Laboratory
Center for Cancer Research
National Cancer Institute
Bldg. 538, Room 209A
Frederick, MD 21702-1201
+1 (301) 846-1842
wau...@mail.nih.gov
http://mcl1.ncifcrf.gov/waugh.html
--



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] a challenge

[George Sheldrick]

Dear James,

I agree with Pavel that your example is not very realistic. In practice
one would start from the heavy atom positions. As well as providing
starting phases, they are useful in other ways. For example. shelxe
(and probably most other tracing programs) adds them to a 'no-go'
map so it knows where NOT to trace the main-chain.

Best wishes, George


Dear James,

your challenge in its current form ignores an important source
of information for model building that is available for your
simulated data - namely, it does not allow to use anomalous
phase information in the model building. In difficult cases on
the edge of success such as this one, this typically makes
the difference between building and not building.

If you can make the F+/F- and Se substructure available, we
can test whether this is the case indeed. However, while I
expect this would push the challenge further significantly,
most likely you would be able to decrease the Se incorporation
of your simulated data further to such levels that the anomalous
signal is again no longer sufficient to build the structure. And
most likely, there would again exist an edge where a small
decrease in the Se incorporation would lead from a model built
to no model built.

Best regards,

--
Pavol Skubak
Biophysical Structural Chemistry
Gorleaus Laboratories
Einsteinweg 55
Leiden University
LEIDEN  2333CC
the Netherlands
tel: 0031715274414 tel:0031715274414
web: http://bsc.lic.leidenuniv.nl/people/skubak-0



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] a challenge

[George Sheldrick]

James,

I had in fact just come to the conclusion that the indexing was 
consistent with 3dko for 'possible' but not for 'impossible',

which I suppose was logical.

George

Woops!  sorry folks.  I made a mistake with the I(+)/I(-) entry.  They 
had the wrong axis convention relative to 3dko and the F in the same 
file.  Sorry about that.


The files on the website now should be right.
http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz
http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz

md5 sums:
c4bdb32a08c884884229e8080228d166  impossible.mtz
caf05437132841b595be1c0dc1151123  possible.mtz

-James Holton
MAD Scientist

On 1/12/2013 8:25 AM, James Holton wrote:


Fair enough!

I have just now added DANO  and I(+)/I(-) to the files.  I'll be very 
interested to see what you can come up with!  For the record, the 
phases therein came from running mlphare with default parameters but 
exactly the correct heavy-atom constellation (all the sulfur atoms in 
3dko), and then running dm with default parameters.


Yes, there are other ways to run mlphare and dm that give better 
phases, but I was only able to determine those parameters by 
cheating (comparing the resulting map to the right answer), so I 
don't think it is fair to use those maps.


I have had a few questions about what is cheating and what is not 
cheating.  I don't have a problem with the use of sequence 
information because that actually is something that you realistically 
would know about your protein when you sat down to collect data.  The 
sequence of this molecule is that of 3dko:

http://bl831.als.lbl.gov/~jamesh/challenge/seq.pir

  I also don't have a problem with anyone actually using an 
automation program to _help_ them solve the impossible dataset as 
long as they can explain what they did.  Simply putting the above 
sequence into BALBES would, of course, be cheating!  I suppose one 
could try eliminating 3dko and its homologs from the BALBES search, 
but that, in and of itself, is perhaps relevant to the challenge: 
what is the most distance homolog that still allows you to solve the 
structure?.  That, I think, is also a stringent test of 
model-building skill.


  I have already tried ARP/wARP, phenix.autobuild and 
buccaneer/refmac.  With default parameters, all of these programs 
fail on both the possible and impossible datasets.  It was only 
with some substantial tweaking that I found a way to get 
phenix.autobuild to crack the possible dataset (using 20 models in 
parallel).  I have not yet found a way to get any automation program 
to build its way out of the impossible dataset.   Personally, I 
think that the breakthrough might be something like what Tom 
Terwilliger mentioned.  If you build a good enough starting set of 
atoms, then I think an automation program should be able to take you 
the rest of the way.  If that is the case, then it means people like 
Tom who develop such programs for us might be able to use that 
insight to improve the software, and that is something that will 
benefit all of us.


Or, it is entirely possible that I'm just not running the current 
software properly!  If so, I'd love it if someone who knows better 
(such as their developers) could enlighten me.


-James Holton
MAD Scientist

On 1/12/2013 3:07 AM, Pavol Skubak wrote:


Dear James,

your challenge in its current form ignores an important source
of information for model building that is available for your
simulated data - namely, it does not allow to use anomalous
phase information in the model building. In difficult cases on
the edge of success such as this one, this typically makes
the difference between building and not building.

If you can make the F+/F- and Se substructure available, we
can test whether this is the case indeed. However, while I
expect this would push the challenge further significantly,
most likely you would be able to decrease the Se incorporation
of your simulated data further to such levels that the anomalous
signal is again no longer sufficient to build the structure. And
most likely, there would again exist an edge where a small
decrease in the Se incorporation would lead from a model built
to no model built.

Best regards,

--
Pavol Skubak
Biophysical Structural Chemistry
Gorleaus Laboratories
Einsteinweg 55
Leiden University
LEIDEN  2333CC
the Netherlands
tel: 0031715274414 tel:0031715274414
web: http://bsc.lic.leidenuniv.nl/people/skubak-0







--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] a challenge

[George Sheldrick]

I have now looked at James's two challenges to see what I could learn 
from them, and will try to give enough details so that less experienced 
readers of this list can repeat what I did and apply the experience 
thereby gained to solving their own structures. For those who are not 
interested in the details, the bottom line is that SHELXC/D/E can solve 
both 'possible' and 'impossible' almost routinely, starting by finding 
the substructure, without using any information derived from the known 
structure. It should be emphasised that this does not produce a fully 
refined structure, but the resulting poly-Ala trace of about 70% of the 
structure and 'free lunch' maps showing many side-chains would be a good 
starting point for programs (such as Buccaneer or wARP) that dock a 
known sequence and complete the structure. My students would of course 
be expected to complete the map interpretation themselves using the 
excellent facilities available in Coot, that is always very educational!


I used the current SHELX beta-test programs that will shortly be 
released as the official versions.


First i used Tim Gruene's mtz2sca to convert James's mtz files into a 
format that SHELX can read, and then ran SHELXC from the command line to 
make the files possible.hkl (native intensity data), possible_fa.hkl (h 
k l FA and phase shift alpha) and possible_fa.ins (input file to run 
SHELXD (and the same for 'impossible'). Alternatively I could have used 
Thomas Schneider's hkl2map GUI to call SHELXC/D/E. I looked at the 
d/sig row to see where to cut the resolution for finding the heavy 
atoms and decided on 3.5A (SHEL 999 3.5). If I had been able to input 
unmerged data to SHELXC, e.g. as XDS_ASCII.HKL which is always unmerged, 
I would also have obtained a CC1/2 value that would also indicate where 
to cut the resolution. 3.5A corresponded to d/sig of about 1.0 which 
is still rather low, but cutting at even lower resolution tends to give 
less accurate substructures. To compensate for this optimistic choice 
for the rather weak anomalous data, I increased the number of trials 
(NTRY) to 1. These are the two most critical parameters for SHELXD, 
and as it turns out, for the whole structure solution.


However before running the multi-CPU version of SHELXD, since the PDB 
file of the refined structure was available, I ran AnoDe to use the PDB 
file and anomalous data in possible_fa.hkl to check the substructure. 
This told me that for both 'possible' and 'impossible' it should be 
possible to find 12 well-defined sites, and also that the original 
impossible.mtz was inconsistently indexed. AnoDe also outputs a list of 
heavy atoms in SHELX format that can be input directly into SHELXE for 
density modification and tracing. However that would be cheating because 
AnoDe reads the final PDB file to calculate the anomalous density, and I 
was trying to solve the structure without assuming the answer, even 
indirectly. In general a substructure calculated in this way by AnoDe is 
always much more accurate and complete that one found ab initio from the 
anomalous data.


The best SHELXD solutions had CC 34.6 and CCweak 15.0 for 'possible' and 
28.4/13.2 for 'impossible'. I always tell people to aim for at least 
30/15, so maybe I should have done more than 1 tries for 
'impossible' but my wife was getting impatient (I had promised her that 
we could go for a walk in the snow) so I accepted it. I looked at the 
peaklist from SHELXD pretending not to know that there should be 12 
sites. There was a bit of a gap in peakheight 0.53/0.42 between peaks 11 
and 12 for 'possible' and 0.53/0.45 between peaks 10 and 11 for 
'impossible', so for SHELXE I used -h11 and -h10 respectively. However I 
also used the new -z option that refines the substructure before 
starting on the phasing, and as it turns out that increased the number 
of heavy atoms to 12 in both cases and as it happens all 12 were correct 
in both cases. I started shelxe with:


shelxe possible possible_fa -s0.55 -a30 -h11 -z -q -e1

and similarly for 'impossible'. I was expecting problems so I did 30 
cycles autotracing, normally 3 would be enough. I just guessed the 
solvent content (-s0.55), maybe that could be fine-tuned. For SHELXE, 
there is a remarkably consistent rule that if the CC for the trace 
against the native data gets above 25%, the structure is solved. For 
'possible' this happened after 25 tracing cycles, and the final 'free 
lunch' map (-e1) was indeed convincing. However 'impossible' only 
reached a CC of 17% and although the map did not look completely wrong, 
I would not have been able to interpret it. So I changed one default 
parameter (-m30), increasing the number of density modification cycles 
to compensate for the poor starting phases, and ran the job again. CC 
reached 25% after 16 cycles and produced an excellent map and trace. 
Almost certainly, 'possible' would also benefit from the change, but it 
was solved anyway. As Tom 

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

[George Sheldrick]

Dear Huw,

It looks as though you have correctly diagnosed a problem with AMPLE.

For expansion from borderline partial structures, I recommend the latest
SHELXE (on my beta-test server since Jan. 20th)  and experimenting with
the -O and -F switches, e.g.

-F0.9 -O100 -a30

However SHELXE is still a work in progress, so this may change in future
versions.

Best wishes, George


Hi,

I've been running Ample and I'm a bit confused about the input for the 
shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it 
appears that Ample converts the structure factor amplitudes to intensities 
using mtz2various with the FSQUARED keyword as the log file contains the 
following:

Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag
Data line--- OUTPUT SHELX
Data line--- FSQUARED

Fs are squared on output - better to use original Is from TRUNCATE output
  Data line--- END

However then shelxe is run with the command:

shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3

I thought that the -f flag tells shelxe that the input hkl file contains Fs not 
Is so this should not be present?

When I run shelxe with the phaser/molrep solutions and a hkl file generated either 
from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I 
get much lower CCs for the autotracing which makes sense as all of the solutions 
so far are rubbish! The Ample logs contain CCs30 for all solutions which 
doesn't seem correct.

Any information would be greatly appreciated!

Thanks,



Huw




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

[George Sheldrick]

Correct, shelxe does not use the free -R flags, and works just
as well with the original unmerged unctruncated intensities.

George


Hi Ronan,

On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote:


Well spotted! We originally gave structure factors to SHELXE in our testing as for most 
of our test cases we only had F/SIGF available. We were advised to change to intensities 
but somehow in the released version the -f flag remained. I'll make the 
change and put it in a CCP4 update. Ideally we should be using the original intensities 
rather than converting the structure factors so we'll look to adding that as an input 
option.

Thanks for confirming that! Perhaps the option to add a hkl file for shelxe 
would be a useful? Since I use XDS to integrate and scale data it's as easy to 
generate the shelx format hkl file from the unmerged XDS_ASCII.HKL as it is to 
use the merged intensities in the mtz from the 
aimless/truncate/unique/freerflag pipeline. The only issue with this I can see 
is that there will be no freeR flags but I don't think that shelxe uses these 
anyway?

Thanks,


Huw




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

[ccp4bb] SHELX-2013 release and homepage

[George Sheldrick]

As some of you have already discovered, there is a major new release of 
the whole
of SHELX (the first since 1997) complete with a new homepage that should 
make

downloads easier. To obtain the programs, please point your browser to:

http://shelx.uni-ac.gwdg.de/SHELX/

and then 'register' (top of blue menu, upper left). You will then 
receive the password

immediately by email and can then go to 'downloads'. The procedure has been
designed to make life difficult for spammers etc. A little program (in 
FORTRAN
of course) turns the registrations into a sorted users' list, which I 
hand-edit where

necessary before it appears on the homepage, this may take a few days. The
homepage also provides access to extensive documentation, FAQs etc. Please
let me know of any problems (even typos) with the homepage and programs, 
with
so much new material there are sure to be some bugs. The new versions 
replace
all previous versions including beta-tests and almost all the programs 
have been

improved since their last beta-test version (see 'recent changes').

In particular, the new shelxe_2013/2 corrects a couple of serious bugs 
in the

autotracing from MR models and MRSAD present in the beta-test 2013/1.

George


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] SHELX-2013 release and homepage

[George Sheldrick]

After consulting several Mac users, I decided that there were very few 
32-bit Mac operating systems still in use by crystallographers, so (as 
stated on the new SHELX homepage) I am only providing a 64-bit 
executables for Macs. The Mac executables do not run on old Macs with 
PPC processors either. For Linux and Windows I provide both 32 and 
64-bit versions. One problem is that even if I tried to cross-compile a 
32-bit version for Macs (with -m32 on the ifort compile/link command 
line?), I would have no way of testing it, and I would not wish to 
distribute untested programs. It might destroy SHELX's reputation for 
robustness. All SHELX programs in this release are as far as physically 
possible statically linked, which explains why the executables are large 
(though the Intel MKL FFT can take some of the blame for that too). 
Static linking is an essential part of the SHELX 'zero dependencies' 
philosophy.


Apart from some trivial problems like some programs pretending to be 
beta-test versions when in fact they are the final release (I had simply 
forgotten to change the text), the complaint by Zhu was the only 
significant problem reported from the first ca. 500 downloads. There was 
however a problem in registering for the programs via the homepage using 
iPhones, but I think that I have managed to fix that now (I don't 
possess an iPhone or any other cell phone). However I would be very 
grateful to hear if anyone encounters difficulties with the new release 
or the homepage, there is so much new material in the homepage that 
there must be plenty of typos.


George

On 02/27/2013 11:21 PM, James Stroud wrote:

The underlying issue is that the implementation of OS X dynamic linking is 
dependent system architecture. As I understand it, OS X 10.5.8 has a 32 bit 
kernel, so its dynamic linking is not forward-compatible with 64 bit OS X 
versions, for which SHELX-2013 seems to built.

Also, to be fair, it's not as if Linux users have ever been able to migrate 
from from 32 bit to 64 bit without a complete system overhaul.

So while I believe that OS X may not be the optimal OS of the future, the 32/64 
bit incompatibility should not be blamed as the reason.

James


p.s. What I don't understand is why the dynamic loader was ever needed in the first 
place. As a zero dependency program, wouldn't it make sense just to 
statically compile all of the SHEL* programs at the cost of a little bigger downloads?



On Feb 27, 2013, at 3:10 AM, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

phew - and people claim, macs were user-friendly. On Linux you just
add '-static' (at least for command line tools as the shelx programs)
and make the sane assumption that the kernel is less than say 10 years
old...

Tim

On 02/26/2013 04:50 PM, Guangyu Zhu wrote:

I just downloaded it. I'm using Mac 10.5.8 and getting error
messages:

dyld: unknown required load command 0x8022 Trace/BPT trap

Google search shows that:


You should contact the developer of this application. Only the
developer can fix this. The application was incorrectly built on a
OS X 10.6 machine for a OS X 10.5 machine. The developer can fix
this by considering three things:


1. Using the correct compiler parameters: gcc-4.2
-mmacosx-version-min=10.5 -isysroot /Developer/SDKs/MacOSX10.5.sdk
...


2. Using the correct linker settings (setting environment variable
before link command). This is required, so that the OS X 10.6
linker will not use the loader command 'LC_DYLD_INFO_ONLY'
(=0x8022), because OS X 10.5 does not understand this command:

export MACOSX_DEPLOYMENT_TARGET=10.5 (or   setenv
MACOSX_DEPLOYMENT_TARGET=10.5)


After this is fixed, one can check if the application was correctly
built for OS X 10.5 by running 'otool':

otool -l binary

The correct binary should not contain any  'LC_DYLD_INFO_ONLY'
load commands (only 'LC_DYLD_INFO' commands).


(also see my blog article http://grauonline.de/wordpress/?p=71 )



Is it possible to build one for Mac 10.5.8?

Thanks!

Guangyu Zhu

On 2/26/13 3:32 AM, George Sheldrick
gshe...@shelx.uni-ac.gwdg.de  wrote:


As some of you have already discovered, there is a major new
release of the whole of SHELX (the first since 1997) complete
with a new homepage that should make downloads easier. To obtain
the programs, please point your browser to:

http://shelx.uni-ac.gwdg.de/SHELX/

and then 'register' (top of blue menu, upper left). You will
then receive the password immediately by email and can then go to
'downloads'. The procedure has been designed to make life
difficult for spammers etc. A little program (in FORTRAN of
course) turns the registrations into a sorted users' list, which
I hand-edit where necessary before it appears on the homepage,
this may take a few days. The homepage also provides access to
extensive documentation, FAQs etc. Please let me know of any
problems (even typos) with the homepage and programs, with so
much new material there are sure to be some

Re: [ccp4bb] How to use SHELXE to perform phasing and density modification

[George Sheldrick]

Dear Wei,

There is a new SHELX homepage with extensive documentation and downloading
instructions at: http://shelx.uni-ac.gwdg.de/SHELX/

SHELXE requires reflection files name.hkl (native) and name_fa.hkl (data 
for phasing) and
and the heavy atoms in SHELX format in name_fa.res. I recommend running 
SHELXC to prepare
the files and SHELXD to find the heavy atoms, then everything will be in 
the right format. You can

either run the programs from the command line or use a GUI such as hkl2map.

If (as it seems) your heavy atoms come from an isomorphous structure, 
then you can run SHELXC
to read XDS_ASCII.HKL or .sca files to make the .hkl, files followed by 
AnoDe (also part of SHELX) to
read name_fa.hkl and name.ent (your original full PDB file, no just the 
heavy atoms) to make
name_fa.res containing the heavy atom sites from the anomalous map. Then 
you have the files

you need to run SHELXE, e.g.

shelxe name name_fa -a5 -s0.5 -q

but see the documentation for more information about the command line 
switches, e.g. -n for NCS.
The advantage of this is that your final structure will be relative to 
the same origin as your original

PDB file.

Best wishes, George


On 03/15/2013 10:13 AM, Wei Feng wrote:

Dear all,
I have an original sca file with anomalous signal and a heavy atoms 
sites file in PDB format.


PDB FILE :
CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2
SCALE1 0.012857 0.007423 -0.00 -0.0
SCALE2 -0.00 0.014846 -0.00 0.0
SCALE3 0.00 -0.00 0.005329 -0.0
ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S
ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S
ATOM 10 S HAT 10 -59.282 106.437 9.760 0.74 20.00 S
ATOM 84 S HAT 84 -60.153 114.024 15.399 0.52 20.00 S
... ...

Can I use SHELXE to perform phasing and density modification? How to 
do it?

Thank you for your help!
Wei






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] How to use SHELXE to perform phasing and density modification (correction)

[George Sheldrick]

Sorry, a better command line for running SHELXE in this case would have 
been:


shelxe name name_fa -a5 -s0.5 -q -h -z

this ensures that the heavy atoms are refined before calculating the 
initial phases, this often gives
much better maps. If you are not sure whether the space group is P6122 
or P6522, then you should
run shelxe twice, once with and once without -i (which would invert the 
space group and atom

coordinates). It is usually worth trying different solvent contents (-s).

George

On 03/15/2013 11:09 AM, George Sheldrick wrote:

Dear Wei,

There is a new SHELX homepage with extensive documentation and downloading
instructions at: http://shelx.uni-ac.gwdg.de/SHELX/

SHELXE requires reflection files name.hkl (native) and name_fa.hkl 
(data for phasing) and
and the heavy atoms in SHELX format in name_fa.res. I recommend 
running SHELXC to prepare
the files and SHELXD to find the heavy atoms, then everything will be 
in the right format. You can
either run the programs from the command line or use a GUI such as 
hkl2map.


If (as it seems) your heavy atoms come from an isomorphous structure, 
then you can run SHELXC
to read XDS_ASCII.HKL or .sca files to make the .hkl, files followed 
by AnoDe (also part of SHELX) to
read name_fa.hkl and name.ent (your original full PDB file, no just 
the heavy atoms) to make
name_fa.res containing the heavy atom sites from the anomalous map. 
Then you have the files

you need to run SHELXE, e.g.

shelxe name name_fa -a5 -s0.5 -q

but see the documentation for more information about the command line 
switches, e.g. -n for NCS.
The advantage of this is that your final structure will be relative to 
the same origin as your original

PDB file.

Best wishes, George


On 03/15/2013 10:13 AM, Wei Feng wrote:

Dear all,
I have an original sca file with anomalous signal and a heavy atoms 
sites file in PDB format.


PDB FILE :
CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2
SCALE1 0.012857 0.007423 -0.00 -0.0
SCALE2 -0.00 0.014846 -0.00 0.0
SCALE3 0.00 -0.00 0.005329 -0.0
ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S
ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S
ATOM 10 S HAT 10 -59.282 106.437 9.760 0.74 20.00 S
ATOM 84 S HAT 84 -60.153 114.024 15.399 0.52 20.00 S
... ...

Can I use SHELXE to perform phasing and density modification? How to 
do it?

Thank you for your help!
Wei






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] crystallization of synthetic peptides

[George Sheldrick]

As Mark says, structure solution of smallish peptides is not usually as 
easy as one might expect. A number of the small (say up to 50 residue) 
peptides in the PDB were solved by direct methods, but these require 
native data to 1.2A or (preferably) better. If sulfur is present in the 
molecule, SAD is a good choice and does not require such a very high 
resolution, but you need highly redundant data, so a high symmetry space 
group helps. If even one Met is present in the sequence, since you are 
synthesizing the peptides anyway, you can replace it with selenomethionine.


George

On 11/10/2011 09:15 PM, mjvdwo...@netscape.net wrote:

Hans,

Most natural toxins from snakes, scorpions etc are 50+/-some peptides. 
And quite a few of those have been studied and crystallized (see pdb 
for a list). Having worked on one of these structures as a graduate 
student, I can share my experience:
- Purification is harder than you would think. You are talking about  
10kD, usually around 5kD. Many methods (size exclusion, even 
concentration over a simple membrane) don't work as easily as you 
would like.
- I did not have much of a problem crystallizing (i.e. no worse than 
other proteins, maybe even a little easier)

- Crystals tend to diffract well (maybe better than average)
- Structures can be hard to solve; MIR is very difficult because ions 
tend to not go into such crystals easily (because the molecules are 
small and tightly packed?); MR is hard because (again) it does not 
work very well on very small systems
- Crystallization is not necessarily purification - if you have a 
mixture of peptides to start with, it may be harder to crystallize, or 
not: you might get a crystal that is a (random-ish) mixture.
- If you have more than two cysteines in your sequence (natural toxins 
typically do), the additional problem is to get the correct folding 
and disulphide bridges; alternatively it is very hard to discriminate 
between correctly and incorrectly linked disulphides


Finally:
These sequence should be small enough for NMR. That may or may not 
answer your questions, but it avoids your original question.


Mark



-Original Message-
From: H. Raaijmakers hraaijmak...@xs4all.nl
To: CCP4BB CCP4BB@JISCMAIL.AC.UK
Sent: Thu, Nov 10, 2011 8:16 am
Subject: [ccp4bb] crystallization of synthetic peptides

Dear crystallographers,

Because of the low cost and speed of synthesizing 40- to 60-mer peptides,
I wonder whether anyone has (good or bad) experiences crystalizing such
peptides. In literature, I've found up to 34-mer synthetic coiled coils,
but no other protein class. I can imagine that a protein sample with a few
percent random deletion mutants mixed into it won't crystallize easily,
but has anyone actually tried?

cheers,

Hans

Re: [ccp4bb] Anomalous signal for chlorides

[George Sheldrick]

Dear Yuri,

The new program ANODE (J.Appl.Cryst. (2011) 44, 1285-7, Open Access) is 
designed for this and is very simple to use. It may be downloaded from 
the SHELX beta-test server (please email me if you require downloading 
intructions).


George

On 11/26/2011 06:05 AM, Yuri Pompeu wrote:

Hi Boaz,
Yes indeed, the phosphate group of the molecule looks quite beautiful at 1.17A 
and it has a really big peak 18sigma!
Is there a utility for calculating anomalous maps, or is it simply an option in 
the refinement program?

Re: [ccp4bb] shelxD

[George Sheldrick]

SHELXD does not use the solvent content. However since you know how many 
seleniums it found and presumably know how many methionines are in the 
sequence, you can use that to estimate the number of molecules is the 
asymmetric unit. Note that an N-terminal selenomethionine is often 
disordered and so should not be counted, and that there is a twofold 
axis in P43212 that could be used to form the dimer.


I would start by throwing the P43212 sites into the autotracing version 
of SHELXE (with and without -i, just in case it is P41212) and seeing if 
it traces. If one of these two space groups traces appreciably better 
than the other, then you have solved it. At 2.9A the traces will not be 
complete but should be good enough for this purpose. If as seems likely 
you have NCS, you can improve them by using the -n switch.


George

On 12/06/2011 09:16 PM, Tiruttani Subhramanyam, Udaya Kumar wrote:

hi

I have a 2.9 ang selenomet MAD data set integrated in four space groups P4, 
P422, P222 and C222

i had to integrate in all the four space groups as I was stuck in refining the 
model in P422

by using shelxD I found solution in P43, P43212 and p212121 but not in C222

the CC all/weak for them are as follows

P43212 52.51 / 34.57
P43   43.12 / 25.73
P212121   48.63 / 31.74

i donot know how many molecules are there in the asymmetric unit but 
dimerization of the protein  is know from which i can say it could be even 
number.

but matthews coef shows high probability for heptamer. so i used that solvent 
content in all the above runs.

another observation  is that at 3.3 ang resolution the anomalous CC % value are 
39.2, 35.3, 32.5 and 28.4 for p43212, p43, c2221 and p212121 respectively.

in all cases P422 looks better in terms of SHELXC stats. i am afraid that there 
is twinning involved.

could anyone suggest me whether its possible to conclude the right space group 
among them.


With regards
uday



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

Re: [ccp4bb] shelxD: frogot to mention shelxe beta result

[George Sheldrick]

The pseudo-free CC in SHELXE is not a very decisive figure of merit. By 
far the best way is to run the autotracing (e.g. with -a5) and to look 
at the CC for the trace against the native data. A value of more than 
25% is almost always solved.


George

On 12/06/2011 10:02 PM, Tiruttani Subhramanyam, Udaya Kumar wrote:

Hi

I forgot to mention the ShelxE beta results in the previous mail

P43212 with 15 sites: Mean FOM = 0.669 , Pseudo-free CC = 69.59 %

P43 with 36 sites: Mean FOM = 0.674, Pseudo-free CC = 70.19 %

P212121 with 36 sites:  Mean FOM = 0.689 Pseudo-free CC = 72.08 %

thank you

With regards
uday



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

Re: [ccp4bb] New Faster-than-fast Fourier transform

[George Sheldrick]

From the rather non-technical inofrmation available so far, it seems to 
me that it is like leaving out all but the strongest reflections (or 
perhaps the strongest normalized structure factors). This is unlikely to 
improve the quality of structure refinement, the importance of using as 
much data as possible and not leaving out the weakest reflections has 
often been emphasized. This is quite different to data compression of 
music. However there is one case where we are already doing this, namely 
small molecule direct methods or using the same programs to find the 
heavy atoms in SAD and MAD experiments. These programs use only the 
strongest 15-20% of the normalized structure factors (E-values). This is 
possible because the data to parameter ratio is still sufficient, and 
these reflections contain much of the useful information. However the 
Fourier routines used by these programs (at least the ones I wrote) are 
not taking full advantage of the 'sparseness' of the data, so if the MIT 
people have found a clever way of doing this it might still be useful 
for heavy atom location  (though FFTW and the Intel MKL FFT will be 
difficult to beat).


George

On 01/20/2012 06:57 PM, Ethan Merritt wrote:

On Friday, 20 January 2012, Jim Fairman wrote:

New Fourier transform algorithm supposedly improves the speed of Fourier
transforms get up to a tenfold increase in speed depending upon
circumstances.  Hopefully this will get incorporated into our refinement
programs.

http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html

This report is interesting, but it is not immediately obvious to me that
crystallographic transforms are in the class of problems for which
this algorithm is applicable.

 From reading the very non-technical article linked above, I conclude that
a better summary would be New approach to Fourier approximation provides
a very cheap (fast) way of identifying and then discarding components that
contribute very little to the signal.  In other words, it seems to be a
way of increasing the compression ratio for lossy image/audio compression
without increasing the amount of time required for compression.

So if you're doing map fitting while listening to streamed mp3 music
files, perhaps your map inversion will get a slightly larger slice of
the CPU time relative to LastFM.

On the other hand, it is possible that somewhere in here lies a clever
approach to faster solvent flattening.

Ethan

Re: [ccp4bb] No diffraction

[George Sheldrick]

It depends a lot on which home source and which synchrotron, there are 
enormous differences. Goettingen is uniquely well placed because we can 
reach four synchrotrons in a few (3-7) hours by high speed train and in 
theory at least five more with a longer train journey, trains are very 
convenient for transporting crystals. Two of these synchrotrons do not 
give a higher resolution than our home system, but at least they can 
vary the wavelength. However if we think we can see at least two 
reflections at home, of course we take the crystal to a (suitable) 
synchrotron.


George

On 01/26/2012 04:54 PM, Francis E Reyes wrote:

Ditto to Poul's advice.

I've had many many many cases where crystals diffract poorly (or not at all) on 
home sources only to show excellent diffraction at a synchrotron. (Whether or 
not a home source is properly calibrated is probably the biggest issue, but 
that's for another discussion).



On Jan 26, 2012, at 8:33 AM, Theresa H. Hsu wrote:


Dear crystallographers

I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and 
vapor diffusion method in 24 hours but no diffraction at home source. Dissolved 
crystals was confirmed to be the protein with mass spec.

Any suggestions to improve diffraction would be welcome.

Thanking you in advance.

Theresa



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] Lysozyme/Xenon derivatives Phenix.

[George Sheldrick]

Dear Brennan,

Since you accidentally sent your request to the CCP4bb rather than the 
Phenix email list, I suggest that you try SHELXC/D/E, e.g. using Thomas 
Schneider's HKL2MAP, to see if it gets the same answers. These programs 
have solved lysozyme hundreds of times. HKL2MAP will also automatically 
correct the space group for you!


Best wishes, George

On 02.02.2012 17:43, Brennan Bonnet wrote:

Hi all,

I have a strange result using Phenix's AutoSol to look for xenon sites in 
lysozyme.

For a few months now I have been trying to produce xenon derivatives of lysozyme using 
pressures in the range of 50-350psi and time ranges between 5-60min trying to find the 
sweet spot so that this technique can be applied to other proteins.

For each dataset, I AutoSol using phenix and have it look for 2, 3, and 4 xenon 
sites.  I haven't had much success though and typical values when asked to look 
for 2 sites have been Rwork/Rfree = 0.5585/0.5892, CC=0.14, Bayes-CC=6.5 and 
with xenon sites:

(a, b, c, alpha, beta, gamma, space group)
CRYST1   78.870   78.870   36.940  90.00  90.00  90.00 P 41 21 2

(columns after numbering are a, b, c, occ, B factor)
HETATM1 XE   XE  Z   1  48.601  67.475   1.088  0.06  6.58  XE
HETATM2 XE   XE  Z   2  54.986  76.636   2.746  0.11  7.49  XE

which, to me, says that there is no binding (or at least nothing obvious).

I finally got a good result though with 350psi and 5 minutes pressurization.  
After AutoSol, FOM=0.436, Bayes-CC=33.57, Model CC=0.83, 
Rwork/Rfree=0.2843/0.3023, 117/125 residues build and placed.  And even though 
I told it to only look for 2 sites, Phenix went ahead and found 22 sites:

(a, b, c, alpha, beta, gamma, space group)
CRYST1   79.130   79.130   36.920  90.00  90.00  90.00 P 43 21 2

(colums after numbering are a, b, c, occ, B factor)
HETATM1 XE   XE  Z   1   -36.117 -56.764  -1.825  0.18  9.43  XE
HETATM2 XE   XE  Z   2   -54.805 -54.805   0.000  0.14  6.44  XE
HETATM3 XE   XE  Z   3-8.337 -31.695 -16.766  0.08  8.26  XE
HETATM4 XE   XE  Z   4-5.702 -64.959 -35.134  0.05  5.21  XE
HETATM5 XE   XE  Z   5   -9.535 -22.397 -31.839  0.06 14.33  XE
HETATM6 XE   XE  Z   6-7.319 -66.343 -35.123  0.05  6.02  XE
HETATM7 XE   XE  Z   7-8.580 -21.153 -30.274  0.05  7.43  XE
HETATM8 XE   XE  Z   8 -1.494 -29.583  -2.339  0.06  7.36  
XE
HETATM9 XE   XE  Z   9-0.518 -16.483 -16.776  0.05  6.56  XE
HETATM   10 XE   XE  Z  10   -0.464 -29.847  -4.386  0.06  6.04  XE
HETATM   11 XE   XE  Z  11  -1.222 -16.234 -18.952  0.04  6.51  XE
HETATM   12 XE   XE  Z  12   -6.001 -20.380  -4.532  0.05  7.22  XE
HETATM   13 XE   XE  Z  13  -5.169 -27.522 -10.128  0.05  3.54  XE
HETATM   14 XE   XE  Z  14 -11.931 -67.039  -4.699  0.05  7.96  XE
HETATM   15 XE   XE  Z  15  -6.538 -10.408  -3.761  0.04 10.22  XE
HETATM   16 XE   XE  Z  16  -0.458 -23.897 -31.221  0.05  6.85  XE
HETATM   17 XE   XE  Z  17   -3.308 -65.181  -8.754  0.03  8.08  XE
HETATM   18 XE   XE  Z  18 -11.080 -29.129  -2.144  0.04  5.61  XE
HETATM   19 XE   XE  Z  19  -5.720 -73.029  -2.035  0.04 11.24  XE
HETATM   20 XE   XE  Z  20  10.236  60.097  33.822  0.03  5.38  XE
HETATM   21 XE   XE  Z  21 5.980  68.581   3.532  0.03  7.49  XE
HETATM   22 XE   XE  Z  22  11.107  13.277  27.334  0.03  7.10  XE

I'm pretty sure there aren't 22 sites for xenon to bind in lysozyme but it 
looks to me like the top 2 (maybe top 3) are actual sites which is great.
The strange part is that when I use the same data and have Phenix look for 3 or 
4 sites it then only finds 3 or 4 very low occupancy sites and the CC's/R's are 
again all very poor.
Has anyone had this problem or does anyone know what's going on?  This is the 
first success that I'm having with xenon derivatization and it seems to me that 
if Phenix can find 22 sites when asked to find 2 it should have no problem when 
asked to find 3 or 4.

Thanks in advance,
~Brennan~

Re: [ccp4bb] [ccp4]questions about SHELXD

[George Sheldrick]

Dear Lu Yu,

Most readers of this list will only be familiar with the use of SHELXD 
to find heavy atom sites for experimental phasing, but it appears that 
you are using it for small molecule direct methods, which in fact is 
what the program was originally written for. For small molecule direct 
methods you MUST have a resolution at which the atoms are resolved from 
each other, i.e. 1.2A or better, and 1.0A is a big improvement over 
1.2A. For experimental phasing the heavy atoms are further apart and so 
much lower resolution may succeed, I have heard of cases where even 10A 
data were sufficient to find heavy atom clusters.


For small molecule direct methods you will need an name.hkl file 
containing h,k,l,I and sigma(I) (HKLF 4 format) or h,k,l,F and sigma(F) 
(HKLF 3 format), as specified by the HKLF instruction at the end of the 
name.ins file for SHELXD. If possible you should use intensities, most 
integrating and scaling systems can write the HKLF 4 directly without 
going through mtz format. Note that all SHELX programs merge equivalents 
and reject systematic absences as required and that the reflections may 
be in any order.


If SHELXD says  the cell is too small to put atoms randomly then you 
are asking it to find more atoms (the FIND instruction) than fit into 
the asymmetric unit. You should ask for less, check the CELL instruction 
for a typo or maybe you have a salt crystal. Note that the space group 
P1 is specified by LATT -1 and no SYMM cards. If you put in LATT 1 or 
leave it out the space group P-1 will be assumed.


For such a small structure it might be better to use small molecule 
programs for the refinement, otherwise you will have problems when you 
try to deposit and publish the structure. I would (of course) recommend 
SHELXL plus the SHELXLE GUI for this, but you should also try to find an 
experienced small molecule crystallographer to help you to get started, 
almost every chemistry department has at least one. If this does not 
resolve your problems I would be happy to look at your data.


Best wishes, George

On 02/19/2012 12:39 AM, Lu Yu wrote:

Hi all,

I was trying to use SHELXD program for protein peptides (6-7 residues) 
for the very first time, and I got the .pdb file which should be the 
correct solution. However, in the .pdb file, the atoms are labeled as 
ABC and they are not recognized as amino acids.


My question is normally what program can I run after SHELXD, to put 
those atoms into residues in the correct order so that I can use 
refmac to refine the structure?


Another question is, I have another peptide which has P1 space group, 
and the SHELXD won't start and it said the cell is too small to put 
atoms randomly, in this case, can I still use SHELXD for the 
structure solving and what should I do? If not, what other programs 
can I use to solve small peptide structures with 6-7 residues?


Thanks for your help!!

Lu

Re: [ccp4bb] Matthews coeff. from model

[George Sheldrick]

My memory is not as good as it used to be, but I think that I indeed got 
the number of 140 cubic Angstroms per amino-acid from Kevin. It has 
worked fine ever since, and is how hkl2map calculates the solvent 
content for proteins.


George
On 12.03.2012 21:40, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

The number 380A^3/base I gave results from a decent number of nucleic
acids-only PDB files I once analysed with the 'volume' program from
ccp4. I cannot think of an application where knowing the solvent content
must be known to more than 1%, so I bet this number is fine for any such
purposes.

I got the number 140A^3/a.a. from George Sheldrick who told me where he
got this number from, but I do not remember for sure - it could be Kevin
Cowtan, but George may update my memory in order to pay proper credit.

Cheers,
Tim

On 03/12/2012 08:48 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:

I can't imagine the results would be very different for protein-DNA vs. 
protein-RNA.

The reason protein-nucleic acids is an extra category in mattprob is largely 
due to poorer statistics
resulting from limited sample size and hence no reliable resolution dependence 
can be computed.

In addition the partial specific volumes for protein (0.74 cm3/g) and nucleic 
acids (0.50 cm3/g) are
different, so an exact calculation needs to consider their ratio to obtain the 
correct psv estimate

BR

- Original Message -
From: Tim Gruenet...@shelx.uni-ac.gwdg.de
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, March 12, 2012 11:07:29 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] Matthews coeff. from model

Dear James,

I do not know such a tool, but you can use 140A^3/a.a. and 380A^3/base to 
calculate the solvent content by hand.

Regards,
Tim

On 03/12/2012 06:35 PM, james09 pruza wrote:

Dear CCP4bbers,

Is there any tool to calculate the Matthews coefficient from a
crystallographic model of RNA-protein complex?

Thanking you.
James.




- --
Michael C. Thompson

Graduate Student

Biochemistry  Molecular Biology Division

Department of Chemistry  Biochemistry

University of California, Los Angeles

mi...@chem.ucla.edu


- -- 
Dr Tim Gruene

Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.11 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFPXl8gUxlJ7aRr7hoRAnKIAKC9BiLuWTo8j/NOUkKee1FlcOSULACggsPw
uFJo7bCPaZ2mJ/LQcsxkDKU=
=Wzko
-END PGP SIGNATURE-

Re: [ccp4bb] unstable refinement error in SHELXL

[George Sheldrick]

Dear Lu Yu,

SHELXL is usually very stable so there must be an error in your .ins 
file, but it is difficult fo us to guess what it is without seeing the 
full file. A common error that can cause such instability is caused by a 
long-standing bug in Coot, which sets some occupancies in the .ins file 
to 1.0 (meaning that they can be refined freely starting at 1.0) rather 
than the usual 11.0 (which means that they should be fixed at 1.0; you 
can add 10 to a parameter to fix it). Another possibility is that Coot 
has not understood a 'free variable' that has been used for e.g. 
occupancy refinement. The small molecule people use other graphical GUIs 
for SHELXL (shelXle, WinGX, Olex2, System-S, XSEED, Oscail, XSHELL etc.) 
that make far fewer mistakes. The .ins files written by Coot should 
always be checked carefully and if necessary edited before running SHELXL.


Best wishes, George

On 03/19/2012 05:00 PM, Lu Yu wrote:

Hi all,

I was using SHELXL for the refinement of a small peptide molecule (6-7 
residues), and it was working for the first round. But then it gave me 
an error message. I don't know what's going on and have you had the 
same problems? Can you give me some suggestions?


_For more information_:
I was using coot to read in .fcf and .res file, and after model 
building, coot can generate an .ins file. I was using this .ins file 
and the original .hkl for the next round of SHELXL, except I added one 
line ANIS in the .ins file:


DEFS 0.02 0.1 0.01 0.04
CGLS 10 -1
SHEL 10 0.1
FMAP 2
PLAN 200 2.3
LIST 6
WPDB 2
*ANIS*

I checked the working .ins and not-working (generated from coot) .ins 
files,
1)*the working .ins* (generated from .res file at the very beginning) 
has:


WGHT0.10
SWAT1.3527622.1931
FVAR   2.6206  0.5  0.5  0.5  0.5

2) *the not-workind(generated from coot) .ins* has:

WGHT  0.1
FVAR  1.0

*The refinement is shown as follows:*
 Read instructions and data
 ** Warning: unusual EXTI or SWAT parameter **
 ** Warning:8 bad CHIV instructions ignored **
 Data:6342 unique,  0 suppressed   R(int) = 0.   R(sigma) 
= 0.0615

 Systematic absence violations:0Bad equivalents:0
 wR2 =  0.4370 before cycle   1 for   6058 data and  1690 /  1690 
parameters
 GooF = S = 4.279; Restrained GooF =  5.862  for   2243 
restraints
 Max. shift = 0.259 A for O_1131bMax. dU =-0.409 for O_1131b   at 
06:08:24
 wR2 =  0.7365 before cycle   2 for   6058 data and  1690 /  1690 
parameters
 GooF = S =12.229; Restrained GooF = 12.221  for   2243 
restraints
 Max. shift = 0.175 A for O_2131aMax. dU =-0.157 for O_5017at 
06:08:25


 ** REFINEMENT UNSTABLE **



The other peptide dataset also has similar problem:
I was using coot-SHELXL, model building - refinement cycle 
*successfully for the first 3 rounds*, but then, it gave me an error 
message:


 Read instructions and data
 ** Warning: unusual EXTI or SWAT parameter **
 ** Warning: no match for1 atoms in CONN **

 ** CANNOT RESOLVE ISOR .. O  LAST **

I checked the working .ins and not-working  .ins files (both generated 
from coot this case),

1) the *working .ins*:
WGHT0.10
SWAT1.2889323.0398
FVAR   2.6472  0.5  0.5

2) the*not-working .ins*:
WGHT0.10
SWAT1.3447083.0452
FVAR   2.731  0.54231  0.5409

I was really confused, since I was using coot for model building for 
other datasets, and the .ins file generated from coot is good for 
SHELXL, but it didn't work all the time, eg. it work for the first few 
rounds, then there is a problem.


Can you give me some suggestions about what  I should do to get the 
SHELXL running again?


Thanks,
Lu




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] Announcing a Web Server for the Grade ligand restraints generator.

[George Sheldrick]

Dear Gerard,

That will be an extremely useful facility. Is a 'regrading' of the 
monomer library planned, at least for common cofactors and 
crystallization additives?


Best wishes, George

On 03/19/2012 06:22 PM, Gerard Bricogne wrote:

Dear all,

The generation of reliable restraints for novel small-molecule
ligands in macromolecular complexes is of great importance for both ligand
placement into density maps and subsequent refinement. This has led us to
develop Grade, a ligand restraint generator whose main source of restraint
information is the Cambridge Structural Database (CSD) of small-molecule
crystal structures, queried using the MOGUL program developed by the CCDC.
Where small-molecule information is lacking, Grade uses quantum chemical
procedures to obtain the restraint values.

Grade was released to academic users as part of the BUSTER package in
July 2011 and has proved popular. However, a problem for numerous academic
users has been that, in order to get the best restraints from Grade, a CSD
system licence is necessary to make use of MOGUL. Although many institutions
already have CSD site licences, and otherwise licences are available at a
reasonable cost, this has prevented the use of Grade by small groups and
occasional users.

To provide easy access to Grade, the CCDC has kindly agreed that we
can provide a public Web server that includes the use of MOGUL in its
invocation of Grade. The first version of the server is now available, free
of charge, at

http://grade.globalphasing.org

We hope this server will prove useful to academic users. We will be
very grateful for any feedback you might be able to provide about this
server, so that we can keep improving it to meet the needs of the community.
Please send us your feedback and comments at

  buster-deve...@globalphasing.com

rather than write to a specific developer.


With best wishes,

The Global Phasing developers: Gerard Bricogne, Claus Flensburg,
Peter Keller, Wlodek Paciorek, Andrew Sharff, Oliver Smart,
Clemens Vonrhein and Thomas Womack.




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] correlated alternate confs - validation?

[George Sheldrick]

Dear Frances,

I don't think that you can put the blame entirely on the 80 column 
limitation.


The program SHELX76 was limited to 80 columns because the input came as 
punched cards. It introduced a simple concept, the /free variables/, 
that are frequently used to represent occupancies and can be used to to 
build complicated networks of disordered residues with interdependent 
occupancies. Restraints may be applied to linear sums of these free 
variables. Ever since, small molecule crystallographers have used this 
concept to refine the disorders that they frequently encounter.


Best wishes, George



On 07/23/2014 05:20 PM, Frances C. Bernstein wrote:

I agree that it would be excellent to be able to associate
alternate conformations (beyond the individual residue) but
when we defined the PDB format we had an 80-column limitation
per atom and so only one column was allowed for alternate
conformations.  In an ASCII world only 36 characters were available
to define alternate conformations.  This is inadequate to allow
for many residues with independent alternate conformations -
one residue with three conformations would use up 3 of the 36
characters.  Thus there was no way to say that alternate
conformation A in one residue is or is not associated with
alternate conformation A in another residue.

 Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
  *   ***  f...@bernstein-plus-sons.com
 *** *
  *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Wed, 23 Jul 2014, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Bernhard,

That's right, the definition is not in the PDB, but REFMAC sensibly
handles it this way. It is certainly a short-coming if not bug in the
PDB (definition).

Best,
Tim

On 07/23/2014 04:49 PM, Bernhard Rupp wrote:

?? Refmac knows because of the group definition, otherwise I cannot
force grouped occupancy refinement. There is no definition in PDB
that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of
(whatever) residue/water.

BR

-Original Message- From: Tim Gruene
[mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014
15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re:
[ccp4bb] correlated alternate confs - validation?

Hi Bernhard,

do you refer to the PDB who, according to Martyn, remove the altloc
indicator? That's certainly a serious bug that should be fixed as
quickly as possible.

Within refmac the preservation is fine and as you would expect it
to be: altA only sees atoms in altA and those witout altLoc, etc,
which makes sure you PDB file is interpreted correctly by refmac5.
That's how I refmac works.

Best, Tim

On 07/23/2014 03:26 PM, Bernhard Rupp wrote:

I would probably make the two waters alternates of each other.





Quite possible, but the group definition, i.e. to which alt
conf. side chain they belong,



would need to be preserved, too.





BR







Cheers, Robbie



Sent from my Windows Phone



_



Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan:
CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate
confs - validation?



Hi Fellows,





something that may eventually become an issue for validation and
 reporting in PDB headers:





using the Refmac grouped occupancy keyword I was able to form and
 refine various networks of correlated



alternate conformations - it seems to works really well at least
in a 1.6 and 1.2 A case I tried.



Both occupancy and B-factors refine to reasonable values as
expected/guessed from e-density and environment.



Respect  thanks for implementing this probably underutilized
secret.





This opens a question for validation: Instead of pretty much
ignoring any atoms below occupancy of 1, one



can now validate each of the network groups  geometry and density
fit separately just as any other



set of coordinates. I think with increasing data quality,
resolution, and user education such refinements will become more



frequent (and make a lot more sense than arbitrarily setting
guessed independent hard occupancies/Bs



that are not validated). Maybe some common format for
(annotating) such correlated occupancy groups might



eventually become necessary.





Best, BR





PS: Simple example shown below: two alternate confs of residue
338 which correlate with one



water atom each in chain B, with corresponding partial occupancy
(grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4).





occupancy group id 1 chain A residue 338 alt A



occupancy group id 1 chain B residue 5



occupancy group id 2 chain A residue 338 alt B



occupancy group id 2 chain B residue 16



occupancy group alts complete 1 2



. more similar



occupancy refine





AfaIct this does what I want. True?

Re: [ccp4bb] Twinning in space group Pc

[George Sheldrick]

Dear Kristof,

Have you tried to solve it with the new SHELXT? You can force it to 
consider only chiral (Sohnke) space groups by putting -c on the command 
line.


Best wishes, George




On 13.08.2014 11:00, Kristof Van Hecke wrote:

Dear,

I’m struggling with the following (small molecule) problem:

We are trying to solve the structure of a metal-organic framework containing a 
chiral compound.
The space group is most probably Pc, but when refining, SHELX gives the error 
“Possible racemic twin or wrong absolute structure - try TWIN refinement”.
As we know our compound is enantiopure, a racemic twin is very unlikely. In 
this regard, also a centro-symmetric space group is not possible (although 
CrysAlisPro always gives P2/c as the proper space group). As a matter of fact, 
trying different space groups is not solving the problem.

The second problem is that half of the structure is visible, but the other half 
is completely not clear. Refinement is not possible at all (R-value of 33%).
When running TwinRotMat (Platon), I get the following possible 2-fold twin axes:

2-axis (   0   1  -1 ) [  -2   5  -4 ], Angle () [] =  2.31 Deg, Freq =14
 *
(-0.992   -0.0190.015)   (h1)   (h2)   Nr Overlap =84
(-0.4300.075   -0.860) * (k1) = (k2) BASF =  0.96
( 0.459   -1.146   -0.083)   (l1)   (l2)DEL-R =-0.064
  
2-axis (   0   1   1 ) [   2   5   4 ], Angle () [] =  2.31 Deg, Freq =15

 *
(-0.9920.0190.015)   (h1)   (h2)   Nr Overlap =   229
( 0.4300.0750.860) * (k1) = (k2) BASF =  0.94
( 0.4591.146   -0.083)   (l1)   (l2)DEL-R =-0.050
  
2-axis (   1   0  -2 ) [   3   0  -2 ], Angle () [] =  0.54 Deg, Freq =19

 *
(-0.1360.000   -0.576)   (h1)   (h2)   Nr Overlap =   992
( 0.000   -1.0000.000) * (k1) = (k2) BASF =  0.86
(-1.7030.0000.136)   (l1)   (l2)DEL-R =-0.030
  
2-axis (   1   2  -1 ) [   5   5  -1 ], Angle () [] =  0.39 Deg, Freq =13

 *
(-0.3800.620   -0.124)   (h1)   (h2)   Nr Overlap =   854
( 1.2560.256   -0.251) * (k1) = (k2) BASF =  0.88
(-0.617   -0.617   -0.877)   (l1)   (l2)DEL-R =-0.019
  
However, none of these do actually improve the refinement.



Has anyone encountered possible twinning/twin laws in Pc please?
Or any other suggestions are most welcome?


Thank you very much

Kristof




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Calculating anomalous Fourier maps

[George Sheldrick]

You might consider using AnoDe (J. Appl. Cryst. 44 (2011) 1285-1287). 
This program and its documentation are available via the SHELX homepage. 
You will need a PDB file name.pdb of the native structure and a file 
name_fa.hkl that contains the anomalous differences. You can use SHELXC 
or XPREP to make this file but the easiest way is to run hkl2map and 
pretend that you are going to solve a structure by SAD phasing. This in 
turn requires a reflection data file XDS_ASCII.HKL from XDS or a .sca 
file from HKL2000, Tim Gruene's mtz2sca or the Aimless option output 
polish unmerged (as a processing option under Integration).


Then you can run AnoDe by:

anode name

which produces a file that Coot can display as a map plus a lot of 
useful information about the anomalous density.


George


On 08/29/2014 08:43 PM, Alexander Aleshin wrote:

Could anyone remind me how to calculate anomalous  difference Fourier maps 
using model-calculated phases? I was doing it by
(1) calculating PHcalc from a pdb file using Sfall, then
(2) merging PHcalc with Dano of experimental SFs, then
(3) calculating a map with Dano and PHcalc using FFT program of CCP4.

Now, I've read Z. Dauter's et all paper 
http://mcl1.ncifcrf.gov/dauter_pubs/175.pdf, and it said that their anomalous 
maps were calculated using (delF, PHcalc-90degrees). Why did they use  -90 
degrees?  How does it relay to a (delF, phcalc) map?

Thank you for an advice.

Alex Aleshin



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Space group numbers

[George Sheldrick]

The strange thing is that small molecule crystallographers do not suffer 
from this problem, because they don't use space group numbers! This is 
just as well, because instead of just 8 combinations of primitive 
orthorhombic space groups and settings, they have to consider 111  (if I 
have counted correctly).


George


On 10/02/2014 11:50 AM, Frank von Delft wrote:
I second that!  The default should be symmetry based... cells stretch 
and shrink, but symmetry is harder to change.  (i.e. from crystal to 
crystal.)


(I thought all CCP4 programs have supported this for ages.)



On 02/10/2014 10:25, Kay Diederichs wrote:
On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans 
p...@mrc-lmb.cam.ac.uk wrote:


Be careful: the International Tables space group number may be 
ambiguous. For example sg number 18 may refer to P 21 21 2 or its 
permuted settings P 21 2 21 or P 2 21 21, if you follow the proper 
IUCr convention that primitive orthorhombic space groups have abc
I would like to point out that there is an alternative interpretation 
of the International Tables (Vol A, 4th ed. 1995). In that 
interpretation (which e.g. XDS follows) space group 18 has the 
'standard' space group symbol, P21 21 2 (bold letters in Table 
3.2). This is of course not ambiguous at all; the pure 2-fold then 
corresponds to the c axis and there is always a permuation of axes 
to achieve this. As a result, the axes are not necessarily ordered 
such that abc . The latter ordering is just a convention which 
was chosen for convenience and the convention refer(s) to the cell 
obtained by the transformations from Table 9.3.1 (citing from table 
9.3.2) - in other words, the convention is fulfilled _after_ the 
transformation (which of course is just order-permuting while keeping 
right-handedness) - nothing new here.


In my understanding, CCP4 developers have (years ago) understood this 
convention as a condition, which lead them to  invent CCP4 space 
group symbols 1017 and 2017 as well as 1018, 2018, 3018. This also 
seems to be the reason for the default being SETTING CELL-BASED in 
POINTLESS.


Users of XDS should be aware that by default, POINTLESS therefore 
permutes the axes such that abc . This however may lead to space 
groups 1017 / 2017 / 1018/ 2018/ 3018 - indicated in the MTZ file, 
but not in the POINTLESS log file (last I checked).


In consequence, XDS will use the space group 17 or 18 (which is what 
POINTLESS reports), but the user must provide  the correct ordering 
(which does not necessarily mean abc) of cell parameters in 
XDS.INP. The easiest way, for XDS users, would be to run POINTLESS 
with the SETTING SYMMETRY-BASED option (I wish the latter were the 
default because the default SETTING CELL-BASED has no advantages that 
I can see). Or they use the good old manual way of inspecting, by 
eye, the systematic absences along H00 0K0 00L - this cannot fail.


To me, symmetry trumps cell metric so SETTING SYMMETRY-BASED 
should be the default.


I'm harping on this because I have recently seen how a Molecular 
Replacement solution was not obtained in space group 18 because of 
the misleading (I'd say) ordering abc .


I'm probably also harping on this because it took me so many years to 
discover this failure mode, and I would like to prevent others from 
falling into this trap.


HTH,

Kay



The space group names are unambiguous (though also watch out for R3 
 R32 which are normally indexed as centred hexagonal, but could be 
indexed in a primitive cell)


Phil


On 30 Sep 2014, at 13:07, Simon Kolstoe simon.kols...@port.ac.uk 
wrote:



Dear ccp4bb,

Could someone either provide, or point me to, a list of 
space-groups relevant to protein crystallography just by space 
group number? I can find lots of tables that list them by crystal 
system, lattice etc. but no simple list of numbers.


Thanks,

Simon





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] monitoring refmac refinement

[George Sheldrick]

Dear Alistair,

Erratic behaviour is often caused by the antibumping restraints because 
they get switched off and on, and riding hydrogens and changes in the 
occupancies can affect their action. This probably applies to both programs.


Any suggestions for improving the bulk solvent model in shelxl would be 
welcome, it is clearly inadequate. Since shelxl can now input partial 
structure factors using a/.fab/ file, this might be a good way of 
testing other solvent models.


Best wishes, George


On 10/02/2014 09:07 PM, Alastair Fyfe wrote:
I would be grateful for any advice on how to  obtain  refmac 
information equivalent in detail to the shelxl Disagreeable 
restraints before cycle   N listing. In the later stages of refining 
a set of related structures, I have been alternating between shelxl 
and refmac. Typically this relies on  shelxl for occupancy assignment 
of alternate conformations and associated partially occupied solvent, 
followed by refmac on the shelxl result to improve bulk solvent 
modeling.  Most of the time this two step approach works well and 
yields an  improvement in the final model. However occasionally  the 
refmac step heads in the opposite direction:


  InitialFinal
   R factor0.1156   0.1390
 R free0.1192   0.1477
 Rms BondLength0.0108   0.0110
  Rms BondAngle1.3876   1.8731
 Rms ChirVolume0.1147   0.0979

This seems to happen rather erratically relative to changes in the 
model and I've been unable to determine which restraints/weights are 
responsible.

Thanks for any pointers,
Alastair Fyfe
UCSC




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Space group numbers

[George Sheldrick]

Since this discussion doesn't want to end. I should point out

(a) The IUCr has, in its wisdom, decided to use the */Hall space group 
symbols/* to settle the matter. See International Tables for 
Crystallography, Vol. B (2001), Chapter 1.4, Appendix 1.4.2//and /Acta 
Cryst./ (1981). A*37*, 517-525. These are obligatory input for CheckCIF 
as part of small molecule verification.  'P 21 21 21' becomes 'P 2ac 
2ab' and 'P 21 2 21' becomes equally logically  'P 2ac 2ac'. Fortunately 
for the users, SHELXL-2014 derives the Hall symbols from the symmetry 
operators.


(b) Isn't it time to introduce the 'R 3' or 'H 3' or 'R 3 :H' issue again?

(c) As pointed out already, small molecule crystallographers never have 
this problem because the coordinates of the general position are used to 
define the space group symmetry unambiguously, in conventional settings 
or otherwise. Ian's argument that there could be too much to type in for 
cubic space groups is irrelevant, because the list is always generated 
by a program (e.g. XPREP or its clones).


George



On 10/03/2014 05:13 PM, Ian Tickle wrote:


Hi Kay

On 2 October 2014 15:04, Kay Diederichs 
kay.diederi...@uni-konstanz.de 
mailto:kay.diederi...@uni-konstanz.de wrote:



Once again, citing from ITC Vol A Table 9.3.2 (p. 747 in my 1995
edition) , these conventions refer to the cell obtained by the
transformations from Table 9.3.1. They have been chosen for
convenience in this table. To me, this indicates that abc
_could_ be obtained _if_ one were to transform. But the question
is: why would one want to transform? I don't see sticking to the
original indexing as a convincing convenience.


I'm sorry, unfortunately my edition of ITC-A (5th Ed., 2002) is later 
than yours (4th Ed.) and I have been unable to get hold of a copy of 
the edition that you refer to.  In my edition the table equivalent to 
your 9.3.2 seems to be 9.3.4.1 on p.758 and there doesn't seem to be a 
table equivalent to your 9.3.1 (the only other table in that section 
is 9.3.5.1 but that doesn't seem to be relevant).  Also I am unable to 
match up the text that you quote with what I see in my edition: it 
seems to be completely different.  So it's very difficult to comment.  
According to the Foreword The present 5th Edition is much more 
extensively revised than any of its predecessors ... so I can only 
assume that the text that you quote was considered unclear and was 
removed.  But I agree that if one is concerned with a specific 
structure without reference to any other structure, why would one want 
to transform anything?  It makes no sense.  The conventional setting 
is selected according to table 9.3.4.1, end of story.



My copy of ITC Vol A says (p 41) about Table 3.2: the 'standard'
space group symbols ... are printed in bold face. The Table has
P 21 21 2 (18) and P 2 2 21 (17) in bold face. There is no
ambiguity here.


Again I'm sorry but I don't see that text in my edition (p.41 is just 
a list of references for Chap. 2) and I can't find the corresponding 
section in my Edition.  However I do agree that the standard symbol 
for each space group is printed in bold face in the top-left corner of 
each double-spread page dealing with that space group (also in smaller 
type in the top-right corner).  Perfectly true observation I agree but 
how is it relevant?  The 230 standard symbols are the names of the 230 
equivalence classes defined on the complete set of possible alternate 
settings for the equivalence relations consisting of the possible 
rotations and/or translations relating those alternate settings.  
Since they only serve as labels one could equally well have chosen the 
ordinals 1 through 230 (which are actually given equal prominence to 
the names).


The important point is that the standard symbol is only the _name_ of 
the equivalence class and that this is not sufficient for dealing with 
crystal structures and calculating structure factors etc.: one must 
specify which element of that class, i.e. from the subset of possible 
unique _settings_ that are members of that class, to use.  For example 
in the 5th Ed. the 10 possible settings for standard symbol C2 are 
shown, with the full H-M symbols C121, A121, I121, A112, B112 etc.  So 
e.g. A121 is one of the allowed conventional settings in the 
equivalence class C2.  Notice that the standard symbol C2 is _not_ a 
full H-M symbol: it doesn't need to be, since it's only a name and it 
doesn't need to carry any information.  Its only requirement is that 
it's unique among the 230 equivalence classes.  Similarly the page for 
standard symbol P2221 shows the possible settings (at least in my Ed.) 
P2221, P2212 and P2122.  In this case the standard symbol happens to 
be the same as one of the full H-M symbols of the alternate settings 
but that's not a requirement, any unique name would have done equally 
well.  Also in the setting P2221 there obviously remains an ambiguity 

Re: [ccp4bb] Space group numbers

[George Sheldrick]

Dear Ian, Kay et al.,

The omnipotent CheckCIF program that is used to check all small molecule 
structures submitted to /Acta Cryst./ and many other journals requires 
(a) the H-M space group name, (b) the Hall symbol and (c) the list of 
equivalent positions, and checks that *all three* are consistent!! Ralf 
Grosse-Kunstleve implemented the Hall symbols in cctbx so I presume that 
all Phenix programs understand them.


Each Hall symbol corresponds to a list of general equivalent positions.  
However Hall symbols are not a perfect solution because (a) it is 
possible to have more than one Hall symbol for the same set of 
equivalent positions and (b) although the lists of possible Hall symbols 
are rather extensive, they do not cover all possible combinations of 
space groups and settings. For example the IUCr and Ralf's lists include 
the common non-standard setting P21/n (Hall: -P 2yn) for space group 
P21/c (Hall: -P 2ybc) but not the more rarely used non-standard setting 
B21/d of the same space group. In terms of equivalent positions this 
setting causes no problems, the SHELX notation for it is:


LATT 6
SYMM 3/4+X, 1/2-Y, 1/4+Z

So I have obstinately insisted for the last 40 years that the list of 
equivalent positions is the best way of specifying symmetry. It would 
have saved a great deal of confusion.


I also do not accept the argument that a list of equivalent positions is 
error prone. Firstly they are almost always put there by a program, not 
a human being, and secondly SHELXL and other programs check them for 
internal consistency.


Best wishes, George



On 10/03/2014 07:58 PM, Ian Tickle wrote:



(a) The IUCr has, in its wisdom, decided to use the */Hall space
group symbols/* to settle the matter. See International Tables for
Crystallography, Vol. B (2001), Chapter 1.4, Appendix 1.4.2//and
/Acta Cryst./ (1981). A*37*, 517-525. These are obligatory input
for CheckCIF as part of small molecule verification.  'P 21 21 21'
becomes 'P 2ac 2ab' and 'P 21 2 21' becomes equally logically  'P
2ac 2ac'. Fortunately for the users, SHELXL-2014 derives the Hall
symbols from the symmetry operators.


I agree that would make a lot more sense but it's taken many years to 
get to where we are now so I can't see this happening any time soon!



(b) Isn't it time to introduce the 'R 3' or 'H 3' or 'R 3 :H'
issue again?


Yes by all means: the H cell in ITC (triple cell) means something 
completely different from the PDB idea of H cell, so it's the PDB we 
have to tackle.  But again, realistically is it going to happen?



(c) As pointed out already, small molecule crystallographers never
have this problem because the coordinates of the general position
are used to define the space group symmetry unambiguously, in
conventional settings or otherwise. Ian's argument that there
could be too much to type in for cubic space groups is irrelevant,
because the list is always generated by a program (e.g. XPREP or
its clones).


I assume that the Hall symbol unambiguously defines the list of 
g.e.p.s (if it doesn't then what use is it?).  Assuming that it does 
then why not use it in place of the list and look up the g.e.p.s from 
a file (e.g. syminfo.lib)?  As I said before, comparing lists of 
g.e.p.s seems to be overkill and prone to errors (and in fact I think 
there have been bugs in the CCP4 implementation).  Simple comparison 
of the Hall symbols would appear to be a lot less error-prone!


Cheers

-- Ian


George




On 10/03/2014 05:13 PM, Ian Tickle wrote:


Hi Kay

On 2 October 2014 15:04, Kay Diederichs
kay.diederi...@uni-konstanz.de
mailto:kay.diederi...@uni-konstanz.de wrote:


Once again, citing from ITC Vol A Table 9.3.2 (p. 747 in my
1995 edition) , these conventions refer to the cell obtained
by the transformations from Table 9.3.1. They have been
chosen for convenience in this table. To me, this indicates
that abc _could_ be obtained _if_ one were to transform.
But the question is: why would one want to transform? I don't
see sticking to the original indexing as a convincing
convenience.


I'm sorry, unfortunately my edition of ITC-A (5th Ed., 2002) is
later than yours (4th Ed.) and I have been unable to get hold of
a copy of the edition that you refer to.  In my edition the table
equivalent to your 9.3.2 seems to be 9.3.4.1 on p.758 and there
doesn't seem to be a table equivalent to your 9.3.1 (the only
other table in that section is 9.3.5.1 but that doesn't seem to
be relevant).  Also I am unable to match up the text that you
quote with what I see in my edition: it seems to be completely
different.  So it's very difficult to comment.  According to the
Foreword The present 5th Edition is much more extensively
revised than any of its predecessors ... so I can only assume
that the text that you 

[ccp4bb] SHELX for Macromolecules Course

[George Sheldrick]

Immediately after the DGK Meeting in Goettingen, there will be an IRTG 
Methods Course
on Macromolecular Applications  of SHELX there on the afternoon of 
Thursday March 19th.

See: http://shelx.uni-ac.gwdg.de/SHELX/workshops.php  for details.

George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] extracting PHENIX structures

[George Sheldrick]

Dear George and Patrick,

It is particularly tricky to do such a search for SHELX because there 
are different ways of referencing it for refinement (SHELX, SHELX-76, 
SHELXL, SHELXL-97, SHELXL-2014 etc.) and there are other ways of using 
SHELX, in particular SHELXD for finding the heavy atom substructure in 
experimental phasing and SHELXE for improving borderline MR solutions. 
SHELXC/D/E are also often used in pipelines (hkl2map, ccp4i, Arcimboldo, 
Amber etc. and many beamline pipelines), and so may or may not be 
explicitely referenced in the PDB file.


My private estimate of the real figure for SHELX refinement of 
macromolecules in 2014 would be well under 1%, but for refinement of 
small molecules it must be closer to 90%.


Best wishes, George



I did the same search as above (Patrick).

I am confused how with SHELX you can get 320 (when using SOFTWARE) and 
then when using TEXT only 130.


I get the same no's.

If the word SHELX exists as follows
SOFTWARE USED: SHELX

the same word (SHELX) will be picked up when we do a text search as 
well (Its there in the remarks section under software !) But obviously 
NOT !


I can understand is text search gave a higher no but in this case 
software gives more entries.


I can also understand if one PDB id is retuned for multiple searches 
but one keyword search (software or text) the same no must be returned.


I am a bit confused in the big disparity in no's 130/320

In both cases WITHOUT software/text word for SHELX I get 552 1.0A 
X-ray structures of protein only.



On Sun, Jan 25, 2015 at 5:57 AM, Kay Diederichs 
kay.diederi...@uni-konstanz.de 
mailto:kay.diederi...@uni-konstanz.de wrote:


Two additions:
a) SHELXL accounts for 16 X-Ray depositions in 2014; 2 of them
also use Phenix.
b) one can select Does NOT Contain: instead of Contains:.
Excluding, in this manner, SHELXL, Phenix, Refmac, Buster and CNS,
one gets  12 entries. These employ mostly CNX, but also coot (!),
X-PLOR, PRIMEX (?), and one more REFMAC (4OM5) which for some
reason does not show up in the earlier Refmac search.
This shows that the results must be taken with some caution.

Kay





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] .raw file from SAINT to pointless

[George Sheldrick]

Dear Georg,

When you start SADABS, the first question is whether you rquire 'expert 
mode'. This mode asks more questions to set additional parameters. If 
you select expert mode, the second question is the maximum number of 
reflections. 200 is merely the default value. I would be interested 
to hear which important 'merging statistics' are output by Phenix but 
not SADABS+XPREP.


Best wishes, George


On 01/06/2015 01:41 AM, Georg Mlynek wrote:

Dear George and Phil, thanks a lot for the fast answers. Things are 
unfortunately a bit more complicated and the usually very convenient way using 
SAINT-SADABS-XPREP has too much limitations for this datasets because

1. It starts with that one datasets has more than 2.000.000 reflections (space 
group P1, high redundancy and high resolution), so I already have to split the 
initial datasets in two. (SADABS can just process 2.000.000 reflections, 
probably something archaic from old days, when computers were not so fast?)

2. I can then of course combine them with xprep but the XPREP (version 2014/2) 
writes out just merged .sca file. Other formats hkl4, hkl3 are unmerged but can 
be just used with the command line version of xtriage and phenix merging 
statistics (which is a part of the phenix suite and needs additional inputs 
(spacegroup). However as aimless writes out all the statistics too, it is not 
necessary to run these phenix programs anyhow.

Thank you both of you again, for the great programs and support.
@Phil I will send you the SAINT manual and a small raw file offlist.
@George can I write out unmerged .sca files from xprep and does it also print 
out CC*?

(Of course I always use the latest ccp4, but I hoped the old one might work in 
my case).




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] .raw file from SAINT to pointless

[George Sheldrick]

Dear Georg,

Since you collected your data on a Bruker machine and integrated them 
with SAINT you should simply scale the .raw files with the Bruker 
program SADABS and then read them into into XPREP. This can scale the 
two datasets together and produce either merged or unmerged but scaled 
data. The current version calculates the various correlation 
coefficients as a function of resolution and can display them 
graphically. Since you have two separate datasets, you should also 
calculate the CC between them. XPREP can also prepare the files for 
experimental phasing with shelxc/d/e. If you need further help you may 
contact me directly.


Best wishes, George


On 01/05/2015 06:07 PM, Georg Mlynek wrote:




Dear all, I have collected 2 datasets (space group P1, resolution 1.4) on a 
bruker machine using Proteum2 v2014.9-0 software. I integrated both datasets 
with SAINT and would like to continue with Pointless - SCALA - Truncate to 
finally get*scaled but unmerged data*  to be able to calculate CC*, CCanom, 
 .

Pointless should be able to read .raw data (documentation) 
andhttp://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Bruker_data. 
However it fails with the error message

Release Date: 6th January 2014

 **
 **
 * POINTLESS  *
 *   1.8.17   *
 **
 *   Determine Laue group from unmerged intensities   *
 * Phil Evans MRC LMB, Cambridge  *
 * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
 **
 **

  Spacegroup information obtained from library file:
  Logical Name: SYMINFO   Filename: 
/home/georg/ccp4/ccp4-6.4.0/lib/data/syminfo.lib

***
* Information from CCP4Interface script
***
The program run with command: /home/georg/ccp4/ccp4-6.4.0/bin/pointless
has failed with error message
pointless: /home/marcin/series-64-dt/checkout/pointless/sca_unmerge.cpp:1201: 
std::vector SCAIO::SaintRun::MakeBatch(const float): Assertion `BHeader.num  
0' failed.
***

#CCP4I TERMINATION STATUS 0 pointless: 
/home/marcin/series-64-dt/checkout/pointless/sca_unmerge.cpp:1201: std::vector 
SCAIO::SaintRun::MakeBatch(const float): Assertion `BHeader.num  0' failed.
#CCP4I TERMINATION TIME 26 Dec 2014  23:15:29
#CCP4I MESSAGE Task failed


The  strange thing is that it works with an insulin dataset (using Input 
reflection filetyp XDS) and that in the Input reflection filetyp one can just choose MTZ, 
XDS or scalepack, and not SAINT (raw).

I would be grateful if somebody could point me in the direction where the 
problem is or show me an alternative route.

Best regards Georg.




--
Mlynek Georg
University of Vienna
Department of Computational and Structural Biology Max F. Perutz Laboratories
Campus Vienna Biocenter 5 level -2
1030 Vienna Austria

e-mail:georg.mly...@univie.ac.at
mobil: +43 660 42 195 07
office: +43-1-4277-52263



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Absorption correction in small molecule crystals

[George Sheldrick]

Dear Finke,

SADABS and similar programs work best when given scans about several 
axes relative to the crystal. Scanning about a single axis can do more 
harm than good especially if the symmetry is low. SADABS can also do a 
face-indexed numerical absorption correction too, but this assumes that 
the crystal is uniformly bathed in the beam, which is unlikely to be the 
case with highly focussed beams.  Why don't you use the PSI PRIGO 
goniometer to scan about several axes?!


Best wishes, George


On 03.03.2015 17:35, Finke Aaron (PSI) wrote:

Dear comrades,

This is slightly off-topic but there are enough experts here to warrant asking. 
Here at SLS I occasionally get asked to collect small molecule data on the 
synchrotron. By convention, post-refinement corrections for X-ray absorption by 
the crystal are required for publication in Acta C and E. XDS, to my knowledge, 
does not do this, it just corrects for other absorption sources like air. 
Currently, the most popular absorption correction method for small molecules is 
the psi-scan correction implemented in programs like SADABS, but I am wondering 
if SADABS is appropriate for data collected on a single axis, as most 
synchrotron data is. Also, since we use photon-counting detectors (Pilatus), 
the other correction options for CCD detectors probably aren’t appropriate 
either. I rarely if ever see an improvement in R-factors nor other improvements 
in disagreeable reflections after using SADABS from data collected here. What 
does everyone think? Is psi-scan appropriate, or should I resort other methods?

Any insights would be much appreciated.

Best regards,
Aaron
--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Phaser going into infinite loop in Ample

[George Sheldrick]

Dear Dale,

Isabel Uson's ARCIMBOLDO-LITE works well for coiled coils and has the 
same resolution
requirements (2.1A or better) as AMPLE because both use SHELXE to expand 
the solution.
It also employs PHASER to place a small fragment but it is often 
sufficient to let it search for

just two or three copies in the asymmetric unit.

Best wishes, George


On 04/22/2015 06:56 AM, Dale Tronrud wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


We are having a problem with AMPLE and hope someone can help.

The protein is about 70 amino acids long and we suspect it forms a
coiled-coil.  Our previous attempts at molecular replacement have
failed so we hoped that AMPLE, with its ability to generate a variety
of potential models, would do the trick.

Our problem is that all of our CPU cores are consumed by Phaser
jobs that are not making progress.  With this protein Phaser decides
that it will look for 11 copies in the asymmetric unit.  For a few of
the possible ensembles it fails to find even one copy and gives up.
That's fine with us.  For other ensembles it finds a handful of
possible first positions, goes on to look for a second and fails, then
goes back to try to place a second copy again.  We presume that the
intent is to lower the acceptance criteria in the second pass, but in
actuality Phaser simply repeats the same search that failed before and
fails again.  The leads to an infinite loop.

Once all the cores are occupied in this futile endeavor AMPLE makes
no further progress.

How can we get Phaser to either try harder to place a molecule or
to give up?

We are using CCP4 6.5.008 and the copy of Phaser that came with it.
  We used CCP4i to create a script which we modified slightly and ran
using the at command.  The command is:

/usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample
- -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz
- -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence
/user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0
- -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir
/usr/local/rosetta-3.5 -frags_3mers
/user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers
/user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False
- -F F -SIGF SIGF -FREE FreeR_flag  -early_terminate True   -use_shelxe
True -shelx_cycles 15 -use_arpwarp False

Any help is appreciated,
Dale Tronrud
Sarah Clark
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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] SHELX expired?

[George Sheldrick]

Dear Tom,

Please go to the SHELX homepage (Google knows where that is) and 
'register'. You will then immediately
receive an email with downloading instructions (free for academic use). 
Sometimes this email lands in the

trash folder.

Best wishes, George


On 04/18/2015 11:40 AM, Tom Wong wrote:

Dear everyone:

I'm a acdamic user of shelx.

My downloaded shelx from shelx homepage keeps telling me it has 
expired and could not proceed.

(Especially in phasing by HKL3000)

Does anyone encounter such a problem?

I would like to know how to download the updated shelx-2015 version.

There seems to be only shelx-2014 links on shelx homepage.

(PS: I could change the system time and date, but other modules such 
as ARP/wARP would not work with an old date)



Thank you!



Nan Wang

Beijing Normal University




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] SHELXL refinement with TYR on special position

[George Sheldrick]

Dear Francis,

You need to put the atoms starting with CG into PART -1 to prevent them 
clashing, and reset the occupancies to 10.5 (i.e. fixed at 0.5). There 
must be another disorder component pointing somewhere else (also with 
half occupancy).


SHELXPRO has been made obsolete by Anna Luebben's PDB2INS.

Best wishes, George


On 01/24/2017 11:09 PM, Francis Reyes wrote:

Hi all

I'm trying to refine a structure with a tyrosine sitting on a special position 
, or maybe it's some disorder.. or  Suggestions?

https://i.imgsafe.org/7cfbf83a38.jpg


Using just FLAT, CHIV,DFIX, and DANG from shelxpro doesn't work.

Thanks,

Francis




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Proper way to handle multiple conformations of ions/waters

[George Sheldrick]

Dear Paul,

As you suggest, small molecule crystallographers are used to such 
complicated situations and often use SHELXL for the purpose. Since you 
fortunately have 1.0A data you could do the same, first using pdb2ins to 
convert your PDB file to a SHELXL .ins file. You will need to use PART 
instructions to define which atoms belong to which disorder component. 
Then you will probably need DFIX or SADI distance restraints for the 
overlapping atoms and RIGU for the anisotropic displacement parameters. 
SHELXL and pdb2ins can be obtained as part of CCP4 or via the SHELX 
homepage shelx.uni-goettingen.de


Best wishes, George

On 02/21/2017 07:13 PM, Paul Paukstelis wrote:
We've been working on a high resolution (1.0 A) DNA structure that has 
several coordinated magnesium ions that have complete octahedral 
geometry via water or phosphate oxygens but are clearly in multiple 
conformations (which is related to the multiple conformations of the 
coordinating phosphates). Is there a _proper_ way to handle this 
scenario? Should the ions/waters be modeled as independent atoms with 
fractional occupancy, or should they be identified as atoms with 
alternate conformations? The latter case can get complicated for the 
waters as the overlap can make it quite ambiguous in some cases as to 
which two water pairs should be associated as the alternate 
conformers. Perhaps it is a minor point, but I thought there might be 
some kind of convention in the small molecule community where this is 
sure to crop up more often.


Thanks in advance,

--paul




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Parallelization?

[George Sheldrick]

Dear Bernhard,

After Kay showed me how to do it by making SHELXL parallel, I was able 
to make SHELXD, ANODE and SHELXT (my current small molecule direct 
methods program) highly parallel. I'm still working on SHELXE because it 
requires major changes. In principle chain tracing is difficult to make 
parallel because you have  to know what you have already traced.


The talk I gave at the 2016 Computing School in Freudenstadt on the 
subject may be downloaded from the SHELX homepage shelx.uni-goettingen.de


Best wishes, George


On 09.02.2017 22:08, Kay Diederichs wrote:

Hi Bernhard,

I parallelized ESSENS, SHELXL, CNS and a few other programs, and wrote a paper 
about it (long time ago, in J. Appl. Cryst I think). It's actually not 
difficult to parallelize with OpenMP, but it needs time - developers seemingly 
rather spend their time on other things.

Automatic parallelization by compiler options helps only in the most trivial 
cases. It is my experience that the code must be adapted to reach a useful 
level of parallelization.

best,

Kay

On Thu, 9 Feb 2017 12:33:05 -0800, Bernhard Rupp  
wrote:


Hi Developers,



I am wondering whether we fully utilize our hardware, and knowing not much
about the finer detail, I'd like to ask a few questions.



Most workstations have 6-12 or more cores, and equipped with plenty of cheap
memory and SSD arrays and some overclocking, these machines

are pretty decent. Some programs, like xds-par which I run under Win10 in a
Fedora/RH VM fully use the cores and are blazing fast.

On WIN10, some like Shelxd also use all the cores.



In principle, almost all multi-solution programs should be able to be
parallelized relatively simple, by spawning threads and combining the

results later (which I could do e.g. with my arp/warp implements).



Unfortunately, also some stuff that could be easily run on multiple cores
like phenix multi-conformer refi, epmr, or similar does not,

or not on Windows. Why not and how difficult is that to change?



Second, even other programs that have nested loops (and who has not) can be
compiled with e.g. the ifort compiler to use multiple

threads and cores on the i7 series, at least. It is just weird to have say
refmac putter along in one core on a de facto semi-idle workstation.



Is (automated) parallelization via compiler directives feasible, also on
Win, what would it bring, how difficult?



Thx, BR



--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 http://www.hofkristallamt.org/

 b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

Many plausible ideas vanish

at the presence of thought

--







--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS

[George Sheldrick]

Dear Kay,

Exactly. That is why we provided two Linux versions (called pdb2ins and 
pdb2ins_oldlinux) on the SHELX server.
So far two versions seem to be enough and for Macs and Windows only one 
version seems to be required. If
anyone finds this to be insufficient, please let Anna know giving 
details of which OS or Linux distribution you

are using.

At the moment we are only providing 64-bit versions of pdb2ins and there 
have been no complaints about that.
This raises the question of whether I am wasting my time providing both 
32- and 64-bit versions of all the SHELX

programs?!

Best wishes, George
CC Anna

On 10/26/2016 05:12 PM, Kay Diederichs wrote:

Hi Phil,

the error message occurs because your glibc is too old for this binary. The 
glibc cannot easily be updated,  it is tied to the distribution, in your case 
RHEL6. A newer kernel does not change this, nor would an update to RHEL 6.8
This is why distributed Linux software should be built on dated distributions.

Best,

Kay

On Wed, 26 Oct 2016 12:11:25 +0100, Phil Evans<p...@mrc-lmb.cam.ac.uk>  wrote:


Hi George

I�m not sure that anyone here is using shelxl but I�ve just updated our general 
64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a 
complaint. Do you understand this? (I should probably ask our local guys)

Our system is
Scientific Linux release 6.7 (Carbon)

./pdb2ins
./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by 
/tmp/_MEIQO85tj/libz.so.1)

best wishes
Phil



On 25 Oct 2016, at 20:31, George Sheldrick<gshe...@shelx.uni-ac.gwdg.de>  wrote:

SHELXL may be used to refine both small and macromolecular structures against 
X-ray or neutron diffraction data, including non-merohedral twins. A new 
version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has 
been well tested by about 20 volunteers to whom I am very grateful. A new 
version of Anna Luebben's program PDB2INS is also available there (for 64 bit 
systems only). PDB2INS makes the preparation of the .ins and .hkl files to run 
macromolecular SHELXL refinements much easier. For most structures deposited in 
the PDB since 2008 these two files can be generated automatically and no 
changes are needed to run SHELXL.

George
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

[ccp4bb] New version SHELXL 2016/6 and PDB2INS

[George Sheldrick]

SHELXL may be used to refine both small and macromolecular structures 
against X-ray or neutron diffraction data, including non-merohedral 
twins. A new version 2016/6 of SHELXL may now be downloaded from the 
SHELX server. It has been well tested by about 20 volunteers to whom I 
am very grateful. A new version of Anna Luebben's program PDB2INS is 
also available there (for 64 bit systems only). PDB2INS makes the 
preparation of the /.ins/ and /.hkl /files to run macromolecular SHELXL 
refinements much easier. For most structures deposited in the PDB since 
2008 these two files can be generated automatically and no changes are 
needed to run SHELXL.


George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

[George Sheldrick]

Just for the record, the Fortran sources for all the SHELX programs are 
identical for Windows (32 or 64 bit), Linux (32 or 64 bit) and MacOSX 
(always 64 bit) except for one line that I need to comment out for 
Windows. I use the Intel ifort compiler for all these platforms. I pay 
the commercial license fee because SHELX is also used by a few firms, 
but I understand that the ifort compiler is now free for academic use. 
Most of my programs use the Intel MKL numerical library that however 
costs money, but I am working on eliminating it. I do all the 
development under 64-bit SUSE Linux and simply compile for the other 
platforms.


George



On 10/14/2016 06:43 PM, Harry Powell wrote:

Hi

On this point, I have (for many years) built my Windows executables on 
a Mac with a cross-compiler; it is possible to install MinGW on a 
Windows box and have gcc, g++, gfortran available. If you want X 
windows & the compilers, you could install Cygwin. However, I'd prefer 
to use a proper Unix-style environment...


On 14 Oct 2016, at 17:31, Patrick Loll > wrote:


How about the ability to compile code? Are there decent compilers 
readily available for Windows? I like being able to write & compile 
the occasional fortran program {hic sunt dinosaurs}, and it’s easy to 
do this on a unix-based platform like OSX.


Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 
(Crystallographic Computing)


On 14 Oct 2016, at 17:31, Patrick Loll > wrote:


How about the ability to compile code? Are there decent compilers 
readily available for Windows? I like being able to write & compile 
the occasional fortran program {hic sunt dinosaurs}, and it’s easy to 
do this on a unix-based platform like OSX.


If your reasoned arguments fail, I have found that many institutions' 
information technology administrators are easily intimidated by a few 
random references to unix (Rsync! Grep! Bash!). Such words seem to 
function as charms that keep evil spirits (i.e. IT administrators) at 
bay.


On 14 Oct 2016, at 11:14 AM, Mark J van Raaij 
> wrote:


Dear All,

our institution requires me to provide a reasoning not to buy a 
Windows computer (I want to buy a new MacOSX system), so I am 
looking for software that does not run or is limited on Windows.


Not available:
(Auto)SHARP
ARPWARP

Available on Windows but with significant limitations
Phenix (no MR-Rosetta, no parallelization)
CCP4 (limitations on file-names)

Please correct me if pertinent and provide additional examples if 
possible.


Gratefully yours,

Mark

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 





---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pat.l...@drexelmed.edu 



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] SAD phasing

[George Sheldrick]

Dear Shijun,

You can find a lot of information about these programs on the SHELX 
homepage, now moved to
shelx.uni-goettingen.de  See in particular the sections "Tutorials & 
talks" and "SHELX Workshops".
Converting the .phs file to .mtz is not needed for looking at the map  
(Coot can read .phs directly),
and is not recommended for refinement. If you convert .phs to .mtz and 
use that for refinement,
if you are not careful the resolution for the refinement may then be 
much better that you actually
measured,  because you are refining against the "free lunch" 
resolution-extended data.


Best wishes, George Sheldrick



On 28.12.2016 11:43, 张士军 wrote:

Dear Kay
 You mean after convert .phs to .mtz ,use the .mtz file refine the initial 
structure model? By the way , what's the difference between this density map 
with the density map modified after phaser-EP density modification? Thanks a 
lot!!!
Best Regard
Shijun


-原始邮件-
发件人: "Kay Diederichs" <kay.diederi...@uni-konstanz.de>
发送时间: 2016年12月28日 星期三
收件人: CCP4BB@JISCMAIL.AC.UK
抄送:
主题: Re: [ccp4bb] SAD phasing

Dear Shijun,

hkl2map is a very nice graphical user interface that makes it easy to use the 
SHELX programs; I've used it successfully around 3A. You find documentation and 
download information for SHELX C/D/E and hklmap in the CCP4 community wiki, at 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SHELX_C/D/E

hkl2map also writes a script, xxx_phs2mtz.csh

#!/bin/csh -f
#
# Shell script for converting phs to mtz-format
# This script was written by HKL2MAP 0.4.c-beta
# f2mtz keeps order of columns
# cad picks up things in a different order and then writes E1...E4
#
# To convert from phs to mtz type:
#./sad_phs2mtz.csh .phs
#
set fname = $1:r
f2mtz hklin ${fname}.phs hklout t_tmp.mtz > t_f2mtz.log < t_cad.log < wrote:


Hello everyone

I am learning phasing SAD data now ,and I got some files(like i.phs ,  .pdb 
,fa.res,   fa.pdb) when I using SHELXC/D/E,and I know  fa.pdb and fa.res (which 
contain heavy atom information) are used for the further solution searching 
,and   .phs file can read by coot. my question are :what is the .phs used 
for(or which step it can be used ?) ,just for check my structure ? Can I 
convert this .phs file into .mtz ,and used it for refinement or model building 
after I found structure solution ? And only the heavy atom site file (fa.pdb)is 
used when I searching my structure solution using software? Can you guys give 
me some software suggestions about solution searching after SHELXC/D/E when the 
data resolution is around 3A? Thanks a lot 

Best Regard

Shijun



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] New version of SHELXE

[George Sheldrick]

A new version 2017-1 of SHELXE is available for downloading from the 
SHELX server. See /recent changes/ on the SHELX homepage at 
shelx.uni-goettingen.de for details. The most important changes 
(contributed by Isabel Uson) should extend the chain tracing to lower 
resolution. Since this requires extra command line parameters, please 
read /recent changes/ before trying it.


George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[George Sheldrick]

Dear Murpholino,

I suspect that the pipelines in CCP4i and CCP4i2 do not include RIP 
phasing (perhaps they should) but you can also run the SHELX programs 
from a command line since you don't like black boxes. SHELXC reads 
XDS_ASCII.HKL files and has some special facilities for RIP, you can 
find them on the SHELX homepage at shelx.uni-goettingen.de -> Wikis & 
manuals -> SHELXC (then go to the end of the page). It is important to 
try several values for RIPW that sets the relative scale of the BEFORE 
and AFTER datasets and can be critical. Under 'SHELX Workshops' you will 
also find a useful account of RIP phasing by Max Nanao from last year's 
ACA Meeting.


Best wishes, George


On 04/28/2017 09:16 PM, Murpholino Peligro wrote:

That's more like a tutorial for XDS :P (thanks though)

The problems:
1) It uses autorickshaw (which is a black box ...guess I'll read the 
paper today) ...

 and
2) my files were not recognized  (MTZ with proper labels ...even the 
XDS_ASCII.HKL files ).


Is it working? Guess I'll try to contact the developers.


Thanks again

2017-04-28 11:29 GMT-05:00 Christian Roth >:


There was a tutorial for MX including UV RIP available from the
HZB in Berlin (BESSY MX group). Have a look at there website. I'm
sure it is still available, or maybe they can send you the files
on request.

Cheers

Christian



Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:

Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere
on the internet?
What programs can do RIP?
-SHELX
-AutoRickShaw
-?

Thanks






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

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

[George Sheldrick]

Dear Graeme,

The WIGL instruction in SHELXL does exactly that, and has some useful 
options.

http://shelx.uni-ac.gwdg.de/SHELX/shelxl_html.php#WIGL

Best wishes, George


On 08/17/2017 05:17 PM, Graeme Winter 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




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312

Re: [ccp4bb] how to run shelx C/D/E using CCP4 GUI on windows

[George Sheldrick]

Just to confirm what Eleanor said: all SHELX programs prefer to be given 
intensities but can accept F if the intensities have been lost. 
Converting intensities to F (e.g. with ctruncate) and back again 
degrades the statistics for the weak reflections and is discouraged. The 
same applies to PHASER and other modern programs.


George


On 05/08/2017 01:19 PM, Eleanor Dodson wrote:
I cant say anything about Windowssystems - jobs are MEANT to run on 
either.


But re Intensities - you will have intensities in an mtz file 
somewhere - all data processing outputs both amplitudes and intensities..


As a rule the conversion for I to F and back does not change the 
stronger intensities much and again as a rule, the SHELX chain will 
work. However the intermediate conversions are best avoided if you 
still have intensities available

Eleanor

On 8 May 2017 at 10:57, chen c > wrote:


Hi everyone,

Can anybody tell how to run shelx C/D/E within CCP4 GUI on windows
system? Moreover, since shelx C/D/E within CCP4 using mtz file
(structure factor) instead of sca file (intensity), would this
matters in tough conditions?

Thank you!

Best regards
Chen




-- 
Cheng Chen, Ph.D. Candidate

Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291 
Fax:+86-10-62773145 
E-mail:che...@xtal.tsinghua.edu.cn


北京市海淀区清华大学生命科学馆201-212室
邮编：100084





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[George Sheldrick]

Dear Murpholino,

I must apologize, there was a mistake in may last email. The critical 
parameter is, as you correctly pointed out, DSCA not RIPW and it is 
necessary to try a range of values for DSCA. For this reason I am CCing 
this to CCP4bb.


As you will be discovering, RIP phasing is not easy. We treat it like 
SIR, but it is complicated by the presence of both positive and negative 
difference peaks caused by radiation damage. Also density modification 
is less effective for SIR and RIP than for SAD phasing. In the case of 
SAD, just replacing negative density with zero improves the phases, but 
this is not true of SIR and RIP, However using the anomalous signal as 
well (RIPAS) helps, similar to SIRAS.


Best wishes, George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

[George Sheldrick]

Dear James.

What small molecule programs report often looks like:

R1 =  0.1550 for   17413 Fo > 4sig(Fo)  and  0.2058 for all   23715 data
R1(Free) =  0.2208 for   1938 Fo > 4sig(Fo) and  0.2766 for all   2635 data

from a well-known small molecule program being (mis)used to refine a 
protein. This clearly shows the influence of the weak outer reflections, 
however if properly weighted they still make a useful contribution to 
the refinement. Although for historical reasons this quotes I>4sigma(F), 
it corresponds to I>2sigma(I) and the structure was refined against 
intensities, not Fs. In the above case, the large gap betwen R1 and 
R1(free) also suggests that the structure has been a over-refined by 
using anisotropic temperature factors with too lax restraints. R1 is 
unweighted and based on Fs, not intensities, but in practice it seems to 
be a more useful criterion than a weighted or unweighted R2 (i.e. based 
on intensities).


Best wishes, George



On 10/16/2017 05:02 PM, James Holton wrote:


If you suspect that weak data (such as all the spot-free hkls beyond 
your anisotropic resoluiton limits) are driving up your Rwork/Rfree, 
then a good sanity check is to compute "R1".  Most macromolecular 
crystallographers don't know what "R1" is, but it is not only 
commonplace but required in small-molecule crystallography.  All you 
do is throw out all the weak data, say everything with I/sigma < 2 or 
3, and then re-compute your R factors.  That is, use something like 
"sftools" to select only clearly "observed" reflections, and feed that 
data file back into your refinement program.  In fact, refining only 
against data with I/sigma>3 is the way macromolecular refinement was 
done up until about 1990.  These days, for clarity, you may want to 
call the resulting Rwork/Rfree as R1work and R1free.


If you do this, and your R1work/R1free are still just as bad as 
Rwork/Rfree, then weak data are not your problem.  You'd be surprised 
how often this is the case.  Next on the list are things like wrong 
symmetry choice, such as twinning masquerading as a symmetry operator, 
or disorder, as in large regions of the molecule that are too fluttery 
to peak above 1 sigma.  The list goes on, but doing the weak-data 
rejection test really helps narrow it down.


-James Holton
MAD Scientist


On 10/16/2017 3:55 AM, herman.schreu...@sanofi.com wrote:


Dear Michael,

Did you ask Phaser to check for all possible space groups? There are 
still I422 and I4 you did not mention. If the space group that came 
out of Phaser is different from the space group used for processing, 
subsequent refinement programs may use the wrong space group from the 
processing. This should be easy to check.


The other suggestion I have is to try a different processing program. 
Although XDS is excellent, I find that sometimes it has difficulties 
with ice rings, which reveal themselves not in the processing, but in 
the subsequent refinement. You may want to try Mosflm or some other 
processing program.


Best,

Herman

*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag 
von *Michael Jarva

*Gesendet:* Sonntag, 15. Oktober 2017 03:09
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [EXTERNAL] [ccp4bb] Another troublesome dataset (High 
Rfree after MR)


To add to the current anisotropic discussion I recently got a dataset 
I’m unable to refine and I’m hoping I could get some help on figuring 
out if there’s anything I can do.


I get a clear cut solution with Phaser using the same protein as 
search model and got a TFZ of >16, LLG >200, and a packing that makes 
sense, so I don’t doubt the solution. However, the maps look 
terrible, more like something I would expect from a 3.65Å dataset 
rather than the 2.65Å it supposedly is.


The dataset merges well in I4122 to 2.65Å with an overall Rmerge of 
5% and a CC1/2 of >0.5 in the outer shell (see the bottom for full 
summary). There is some minor radiation damage but I could cut out 
most of it due to the high symmetry.


Xtriage reports no indication of twinning, but does say that the data 
is moderately anisotropic, so I ran the unmerged data through the 
StarAniso server, which reported the ellipsoidal resolution limits to 
be 2.304, 2.893, and 3.039. Refining with the anisotropically 
truncated data improves the maps somewhat, but I am still unable to 
get the Rfree below 38%. I tried using both phenix.refine and buster 
with similar results.


I’ve considered the choice of space group and tried I41, F222, 
I212121 , and C2, but with the same results, and Zanuda tells me the 
same thing.


Lastly, there is some minor ice rings, so my last try was to exclud 
the ice ring resolutions, but this made little to no difference.


Normally I would just write this off as the data being bad but this 
time all the statistics tell me this should be doable so I’m curious 
what has gone wrong.


Cheers

Michael Jarva

Summary data forProject: XDSproject Crystal: XDScrystal Dataset: 

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

[George Sheldrick]

Over 50 years ago, a Toepler pump that I had glass-blown myself 
developed a crack that caused several kilos of mercury to hit tha 
ceiling and give me a shower. Fortunately I did not then know how 
poisonous it was and suffered no ill-effects


George


On 12.09.2017 19:46, James Holton wrote:

One more correction,

It seems brominated vegetable oil (BMO) really does contain Br atoms!  
I could have sworn I read in some reputable source long ago that the 
process of "bromination" was an old term for general reduction of 
double bonds and did not necessarily involve bromine. Usually 
hydrogen.  I remembered this because I thought it was hugely 
counter-intuitive.  Now, of course, I cannot find that reference. So, 
who am I to pit the validity of my memory against Wikipedia and a long 
list of links to health-nut web blogs?  Guess I was wrong about that.


The Mountain Dew I am drinking right now has a very faint X-ray 
fluorescence peak that could be Br.  Hard to be sure above 
background.  So I will have to get a sample of neat BMO to sit next to 
my shampoo, pepto and sunscreen on my shelf of heavy atom compounds 
that are on the FDA's GRAS list:

https://www.fda.gov/food/ingredientspackaginglabeling/gras/

Remarkably, the MSDS for BMO is less scary than that of ordinary 
vegetable oil.  This raises more than one interesting topic, but the 
most relevant here I think is "bio-availability". Selenomethionine is 
much much more bioavailable than selenium sulfide, which is the active 
ingredient in my dandruff shampoo. Apparently, humans don't absorb it, 
but microorganisms can mistake it for a source of sulfur.


I expect the bio-availability of Hg in pizza is pretty high 
considering how it bio-amplifies in fish, so I stand by my APE. But it 
is always prudent to read the MSDS before you open a bottle, and then 
read the MSDS of something similar just to put it in perspective.


-James Holton
MAD Scientist

On 9/6/2017 12:59 PM, James Holton wrote:
Was just pointed out to me off-list that my anchovy data was off, so 
I just double-checked the FDA website:


https://www.fda.gov/food/foodborneillnesscontaminants/metals/ucm115644.htm 



Turns out the latest number for anchovies is 0.016 ppm, or 0.5 ug per 
ounce (28g).


So, if you use a whole 2 oz can, that's still ~ 1 microgram Hg as the 
Anchovie Pizza Equivalent.


And it looks like one piece of bigeye tuna sushi could be as much as 
~14g*1.816ppm = 25 APEs


-James Holton
MAD Scientist

On 9/6/2017 11:44 AM, James Holton wrote:
Something that could perhaps be of use here is what I like to call 
the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of 
mercury.  According to the Food and Drug Administration website here 
in the USA the average mercury content of anchovies is 0.34 ppm, 
which is about 1 microgram per ounce of fish.  Tuna can be higher, 
but varies a lot from fish to fish.  My point here is that most 
institutions regard the amount of mercury you bring onsite for 
purposes of eating for lunch, be it sushi or pizza, as small enough 
to be negligible.  I tend to agree.  So, one could argue that 1 
microgram of Hg per day is a "safe amount". Especially if you don't 
eat it.


In terms of protein crystals, a 100 micron wide cube has a volume of 
1 nanoliter, and if it were soaked to a final concentration of 50 mM 
Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng.  So, 100 protein 
crystals soaked with Hg add up to roughly 1 APE.  Please note that I 
am in no way encouraging you to eat your protein crystals, and 
especially not the solutions you soak them in.  You should do your 
own APE calculations for those.  But I do think it important to note 
just how tiny the amount of metal in our crystals really is.


Now, mercury is purportedly the second-most-toxic metal after 
Plutonium.  But Pu derivatives are uncommon.  In fact, until 
recently (4zhd) Pu derivatives were unheard of. The authors I'm sure 
will tell you 4zhd involved no small amount of paperwork. But as 
long as you are not working with Pu, you can regard every other 
metal as less toxic than Hg.


Another good example is selenium; by far the most common metal 
derivative.  Although toxic, Se is also a dietary requirement. I 
suppose this is an excellent demonstration of what "moderation" 
really means.  The Recommended Daily Allowance (RDA) of selenium in 
the USA for adult men and pregnant women is 55-60 micrograms per 
day.  In crystals, one Se atom per 100 amino acids at 50% solvent 
comes to an overall concentration of 50 mM.  So, a 100 micron 
crystal contains about 4 ng of Se.  It would take 15,000 such 
crystals to add up to the US RDA.  The synchrotrons I work at don't 
go thought that many crystals every day.  But even if they did, I'd 
stick to my commercially available multivitamin to get my dietary 
selenium.


So, although it is never a good idea to be sloppy with chemicals in 
the lab, I think it is also important to do the math and think about 
not 

Re: [ccp4bb] New version of SHELXE

[George Sheldrick]

Dear Carlos,

You are correct. I reinstalled CCP4 two days ago and also got version 
0044 and that did not incude the new shelxe_2017-1. However the new 
shelxe is definitely on the shelx server. It is a single statically 
linked executable with no dependencies (!) so you can simply replace the 
old file with it by hand (under Linux, 'which shelxe' will tell you 
where it is). The CCP4 people may be worried that the new shelxe will 
break some of their pipelines, but I am not expecting problems. Also 
some of them are at the Meeting in India. However they do need to change 
several of their pipelines to take advantage of the new tracing features 
such as -Q, -B3 and -a (without a number) that are a significant 
improvement at lower resolution. See 'recent changes' on the shelx 
homepage for details.


Best wishes, George


On 08/28/2017 03:40 PM, Carlos CONTRERAS-MARTEL wrote:

Hi George,

thank you very much for your answer, but I think that my updated 
version of ccp4-7.0.0044 is not using this version of shelxe, or am I 
wrong?


Best

Carlos


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312

Re: [ccp4bb] coot shelxl problem

[George Sheldrick]

Dear Abhishek,

Maybe Paul had forgotten that shelxl was designed to read 80 column 
punched cards.
To check against overrun it was checking that column 80 is a blank. I 
may be able to fix
this in the next version of shelxl. For the moment you will have to do 
some hand editing,

e.g. using continuation lines (see the documentation on the shelx homepage).

Best wishes, George



On 11/02/2017 03:34 PM, Abhishek Anan wrote:

Dear all,

I am trying to shelxl module from within coot after adding a few 
waters but get the following error. Is there a work around?


 ** INPUT INSTRUCTION HH1A   2  -1.5879950... IS LONGER THAN 79 
CHARACTERS **


I would appreciate any help.

Thanks
abhishek





--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312

Re: [ccp4bb] update 057

[George Sheldrick]

Dear Charles (and CCP4 users),

I was delighted to see that CCP4 update 057 at last includes Anna 
Luebben's pdb2ins, which we had been requesting for months and is very 
useful for preparing the two input files needed to run shelxl. 
Unfortunately you were too modest to mention this in your email to the 
group, so I am doing so here!


I should also mention that I was out of email contact for three days 
recently because of hardware problems with the old shelx server that is 
on its last legs and will not be fixed next time. Please use my new 
email address gsheldr at uni-goettingen.de in future. The shelx homepage 
moved to shelx.uni-goettingen.de over a year ago and was not affected.


Best wishes, George


On 10.05.2018 12:17, Charles Ballard wrote:

Dear All

This is out, and contains a fix to the nasty truncate bug detailed earlier (hat 
tip to GPL), it is therefore
recommended that this be applied.

Also included are updates to

* aimless
* ccp4i2
* ccp4i
* gesamt
* mrbump
* dials interface

plus some workarounds for changes to web certificate handling (in ccp4.setup-sh 
and ccp4.setup-csh).  This
will need checking on your local installations as local changes may be lost.

Known issue:

Unfortunately, the changes to the setup files have broken the integration 
between ARP/wARP and CCP4.  This
can be recreated by re-running BINARY.setup.  The next update will address this.

Charles


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312

Re: [ccp4bb] Python3 and MTZ

[George Sheldrick]

This discussion has not convinced me to stop using Fortran. FORTRAN66 
programs such as SHELX76 still compile and run unchanged with modern 
Fortran compilers, though I do use a few useful features introduced in 
FORTRAN77 and FORTRAN90 such as character handling and run-time memory 
allocation. The resulting executables also tend to be faster than when 
Python is used, even when it is used to call routines written in C++.


George


On 06.06.2018 20:54, Robbie Joosten wrote:


Right you are Kay. It would be very weird to start developing things 
on Python 2.7 right now. Its days are numbered: https://pythonclock.org/


Cheers,

Robbie

Sent from my Windows 10 phone


*From:* CCP4 bulletin board  on behalf of Kay 
Diederichs 

*Sent:* Wednesday, June 6, 2018 8:47:07 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Python3 and MTZ
Dear Nicolas,

my (our) motivation is purely that when learning Python today, and 
developing something from scratch, Python3 appears like the better 
choice (compared to version 2) - provided that basic crystallographic 
libraries can be used.


Just a note (for those whose operating system provides only one of the 
two Python flavours): RHEL7 has Python2 as system library, but Python3 
can be installed in parallel (using "Software Collections"). The user 
makes a choice by setting the PATH variable.


best,

Kay

On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  
wrote:


>Dear Kay,
>
>depending of the motivation to develop in python3 (could be due to an OS
>using python3 by default or you really prefer to work with python3). If
>it's due to the OS, a possible strategy is to use virtualenv
>(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>if python3 is the default version for the OS. It exist probably other
>method to have a contain installation of python2 with all the library 
needs.

>
>I used this strategy (virtualenv) to install ccp4 (with the installer
>which needed python2) on a manjaro linux (Arch based) running python3
>and that works very well.
>
>Nicolas
>
>Nicolas Foos
>PhD
>Structural Biology Group
>European Synchrotron Radiation Facility (E.S.R.F)
>71, avenue des Martyrs
>CS 40220
>38043 GRENOBLE Cedex 9
>+33 (0)6 76 88 14 87
>+33 (0)4 76 88 45 19
>
>On 06/06/2018 14:25, Kay Diederichs wrote:
>> Dear all,
>>
>> I haven't tried to read MTZ files from Python until now, but for a new
>> project in my lab I'd like to do that - and with Python3.
>>
>> Googling around, it seems that iotbx from cctbx is not (yet)
>> Python3-compatible.
>>
>> So, what are my options?
>>
>> thanks,
>>
>> Kay
>
>
>
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--
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Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312




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Re: [ccp4bb] [ccp4bb] Oxford University Press

[George Sheldrick]

Since neither I nor my university can afford Elsevier journals, I have 
no access to papers published in them. In view of their excessive 
profits, for some years I have not submitted papers to them and have 
declined all requests to referee for them. If everyone did that, they 
might reconsider their approach. I am not an Apple fan either - I use a 
more reasonably priced native Linux laptop - but have to give Apple 
credit for innovation.


George


On 07/01/2018 06:57 PM, Patrick Loll wrote:


I think what we should do is not publish in journal families where 
the profit is above 10 per cent. Elsevier is the place to start as 
their profit margins are like those of Apple, and of competition 
there is none.


Elsevier: Like Apple, but without the design sense.


But seriously, Adrian makes an excellent point. And the large profit 
margins wouldn’t be quite so galling, if only the publishers were able 
to provide competent and helpful administrative support; but in my 
recent experience, not-for-profit scientific society journals are 
actually providing better experiences for reviewers and authors than 
the big commercial ones.


Pat

---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology

Drexel University College of Medicine

Room 10-102 New College Building

245 N. 15th St., Mailstop 497

Philadelphia, PA19102-1192USA


(215) 762-7706

pjl...@gmail.com 

pj...@drexel.edu 





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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312




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Re: [ccp4bb] Regarding symmetry notion in coot

[George Sheldrick]

For small molecules, programs such as SHELXT move the structure to be as 
near as possible to the center of the unit-cell, not the origin. Failure 
to do so may cause a 'checkCIF alert'.


George


On 06/21/2018 09:34 PM, John Berrisford wrote:


From a PDB deposition point of view, I echo Paul’s comment. If 
possible, please move your molecule closer to the origin. It helps 
with the curation process and is easier for users of your entry as 
some software struggles with such extreme transformations.


Regards

John


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel: +49-551-39-33021 or +49-5594-227312





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Re: [ccp4bb] Structure solution - hexapeptide

[George Sheldrick]

A particularly useful command line option in SHELXT for such cases is 
-L15 to try all trigonal and hexagonal space groups. SHELXT is included 
in recent CCP4 distributions and is also available with documentation 
from shelx.uni-goettingen.de


George

On 02.08.2018 15:53, Aaron Finke wrote:

Hi Kristof,

Direct methods/charge flipping won’t work if your data quality is poor 
below ~1Å. Take a look at your Rmerge, as Jeffrey mentioned. Small 
molecule crystals have more stringent standards for data quality. If 
your Rmerge is 50% or more, it’s probably just noise and not useful 
for direct methods.


If SHELXT doesn’t work on the full data set, try cutting the data down 
to 0.9 Å or even 1 Å. I have had limited success doing that on some 
particularly bad data sets.  Alternatively, run SHELXD at full 
resolution indefinitely (NTRY 0) until it finds a solution. It could 
take days, but you may get something.


As a last resort, if you think this hexapeptide may have any secondary 
structure, you may want to try ab initio MR with ARCIMBOLDO.


Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu 

On Aug 2, 2018, at 8:53 AM, Kristof Van Hecke 
mailto:kristofrg.vanhe...@gmail.com>> 
wrote:


Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, 
there should be 3 Nmol/asym

- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not 
able to solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s 
hardly any homologous models



Has anyone encountered a similar problem please, and could provide 
any possible solutions?

(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


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Tammannstr.  4
D37077 Goettingen
Germany
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Re: [ccp4bb] Oxford University Press

[George Sheldrick]

Dear Bernhard,

To conclude our conversation, the person who determined and deposited 
the most small-molecule structures was not a 'poor Russian' but almost 
certainly Prof. Allan White of UWA, Perth with 5372. He died in 2016. I 
don't know how many papers he had to review as a punishment.


Best wishes, George


On 04.07.2018 20:30, Bernhard Rupp wrote:


I was just fascinated by the math: 800 x 3 = 2400, and given a

work year of 1600 hrs this makes for 1.5 papers per hr to review…

I don’t remember a reference to anyone specific - YS had only about 
2000 papers –


so maybe there are/were even more prolific candidates 

Best, BR

*From:*George Sheldrick 
*Sent:* Wednesday, July 4, 2018 16:17
*To:* b...@hofkristallamt.org; ccp4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Oxford University Press

Dear Bernhard,

I agree with you sentiments, but was wondering which 'poor Russian 
small molecule crystallographer' you had in mind?


Yuri Strutchkov died in 1995. He was an excellent crystallographer but 
with an efficient team and good connections.


I can't really complain, all the fake Chinese structures in Acta E 
cited SHELX for their refinement.


Best wishes, George

On 04.07.2018 13:54, Bernhard Rupp wrote:

Yes, there is a problem in general with these ‘get rich quick with
user data’

facebookoid sites. Publon seems to be another one and I had what
can be charitably described

as a pretty intense exchange with the dude running it. Nothing can
be free (a concept occasionally alien

to the purist academic) and you just pay with whatever data that
will be exploited as a business model.

That is fine as long as the model is transparent.

In response to an earlier post in this thread, complaining about
review overload is perilous if you

expect to get your own stuff reviewed. If you publish 10 papers a
year, on grounds of reciprocity you

should expect to review about 30. Almost one a week sans
holidays…imagine the poor Russian small molecule

crystallographers on 800 papers a year…nothing beats monopolizing
a resource (diffractometer etc…).

So, millennials, be thankful for the democratization of
crystallography, compliment of the synchrotron

facilities and their diligent operators confined to the
subterranean dungeons of beam line hell.

.

Best, BR

PS: Ad Elsevier: In an apparent acute attack of generosity, the
Cell Press stuff can be shared

through links for 50 days.

https://authors.elsevier.com/a/1XK9D3SNvbqr-6

I am responsible only for pushing the content, not for what
happens with your data….

(at a second thought, don’t crystallographers also practically
live to collect data?)

“To help you access and share this work, we have created a Share
Link – a personalized URL providing *50 days' free access* to your
article. Anyone clicking on this link before August 22, 2018 will
be taken directly to the final version of your article on
ScienceDirect. No sign up, registration or fees are required –
they can simply click and read”

*From:* CCP4 bulletin board 
<mailto:CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Patrick Shaw Stewart
*Sent:* Wednesday, July 4, 2018 12:59
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* Re: [ccp4bb] Oxford University Press

Bernhard, did you know that Researchgate is a controversial
organization?  They have been criticised for encouraging users to
upload copyrighted material, see below.  Their business model also
seems to involve charging a high fee to spam their users - we
tried it once but decided we were just annoying the scientists who
happened to get our message.  (Although I agree with you that
10-yr-old articles are less valuable than recent ones.)

An interesting model for scientific publishing is the
journal/Biology Direct/. Reviewers' names and reports are
published along with the article, and it's up to the authors to
amend their article if they agree with any criticisms.  All you
need is three reports for publication  I sent the journal what I
believed to be a ground-breaking review explaining why we get more
colds in winter than summer (later published in /Medical
Hypotheses/).  I was disappointed that I only got one reviewer to
support my article by writing a report.  But I felt that the
format of the journal would have been be very helpful for a
controversial topic.  Link below.

Patrick

__



/ResearchGate /https://en.wikipedia.org/wiki/ResearchGate#Criticisms

In September 2017, lawyers representing the International
Association of Scientific, Technical, and Medical Publishers
(STM) sent a letter to ResearchGate threatening legal action
against them for copyright infringement and demanding them to
alter their handling of uploa

Re: [ccp4bb] Oxford University Press

[George Sheldrick]

es as high
as £9,634, far above average,[23] and many British universities
pay more than a million pounds to Elsevier annually.[24] The
company has been criticized not only by advocates of a switch to
the open-access publication model, but also by universities whose
library budgets make it difficult for them to afford current
journal prices.

For example, a resolution by Stanford University's senate singled
out Elsevier's journals as being "disproportionately expensive
compared to their educational and research value", which
librarians should consider dropping, and encouraged its faculty
"not tocontribute articles or editorial or review efforts to
publishers and journals that engage in exploitive or exorbitant
pricing".[25] Similar guidelines and criticism of Elsevier's
pricing policies have been passed by the University of California,
Harvard University, and Duke University.[26]In July 2015, the
Association of Universities in the Netherlands (VSNU) announced a
plan to start boycotting Elsevier, which refused to negotiate on
any Open Access <https://en.wikipedia.org/wiki/Open_Access> policy
for Dutch universities.^[27]
<https://en.wikipedia.org/wiki/Elsevier#cite_note-27>  In December
2016, Nature Publishing Group
<https://en.wikipedia.org/wiki/Nature_Publishing_Group>reported
that academics in Germany, Peru and Taiwan are to lose access to
Elsevier journals as negotiations had broken down with the
publisher.^[28] <https://en.wikipedia.org/wiki/Elsevier#cite_note-28>

A complaint about Elsevier/RELX was made to the Competition and
Markets Authority
<https://en.wikipedia.org/wiki/Competition_and_Markets_Authority>.^[29]
<https://en.wikipedia.org/wiki/Elsevier#cite_note-29>

On 2 July 2018 at 08:01, George Sheldrick <mailto:gshe...@uni-goettingen.de>> wrote:


Since neither I nor my university can afford Elsevier journals, I
have no access to papers published in them. In view of their
excessive profits, for some years I have not submitted papers to
them and have declined all requests to referee for them. If
everyone did that, they might reconsider their approach. I am not
an Apple fan either - I use a more reasonably priced native Linux
laptop - but have to give Apple credit for innovation.

George


On 07/01/2018 06:57 PM, Patrick Loll wrote:

I think what we should do is not publish in journal
families where the profit is above 10 per cent. Elsevier
is the place to start as their profit margins are like
those of Apple, and of competition there is none.

Elsevier: Like Apple, but without the design sense.

But seriously, Adrian makes an excellent point. And the large
profit margins wouldn’t be quite so galling, if only the
publishers were able to provide competent and helpful
administrative support; but in my recent experience,
not-for-profit scientific society journals are actually
providing better experiences for reviewers and authors than
the big commercial ones.

Pat


---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology

Drexel University College of Medicine

Room 10-102 New College Building

245 N. 15th St
<https://maps.google.com/?q=245+N.+15th+St=gmail=g>.,
Mailstop 497

Philadelphia, PA19102-1192USA

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pj...@drexel.edu <mailto:pj...@drexel.edu>

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Instruments Ltd.

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 Directors: Peter Baldock, Patrick Shaw Stewart

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[ccp4bb] New SHELX versions and email address

[George Sheldrick]

Here is another attempt from my old email address. I was not registered 
to use the email lists from my

new address, but please use it in future!

New versions of SHELXE, SHELXL and SHELXT and also Anna Luebben's 
program pdb2ins that provides
a quick way of setting up a shelxl refinement given a PDB code may now 
be downloaded via the SHELX
homepage at *shelx.uni-goettingen.de*  Details of the changes may be 
found under 'recent changes' on
the homepage. The old shelx download site has not been updated and will 
be decommissioned soon, it is
on a very old computer that is on its last legs and is subject to power 
outages caused by building work.


*Please also note my new email address gsheldr (at) uni-goettingen.de !*

George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312

Re: [ccp4bb] According correct space group assignment...

[George Sheldrick]

Dear Rafal et al,

With some help from Kay I think that I could find out what is happening
here. SHELXT finds the space group Ibca and solves the structure easily
with default parameters but has difficulty in assigning the elements
because it was not expecting arsenic (!). The data are not very good but
it appears to be a cacodylate with five molecules in the asymmetric unit
and an unknown cation (K gave the best results). I could not find the
structure in the COD. I will send you the atom coordinates in a separate
file but the data would never get through CIFCheck (which you would need
to publish it in Acta E.).

Best wishes, George


On 20.04.2018 15:30, 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


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] shelxe version 2019-1

[George Sheldrick]

SHELXE 2019-1 may now be downloaded from the shelx server at 
shelx.uni-goettingen.de. With default parameters this version traces 
structures with good resolution and phasing power faster, for difficult 
structures see 'recent changes' on the shelx homepage or the summary 
printed when the program is run without data files. Note that the 
previous version expires at the end of 2018.


Isabel and George


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312



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Re: [ccp4bb] buying a cluster

[George Sheldrick]

To put the record straight, despite our efforts SHELXE is not currently 
multiply threaded, but ARCIMBOLDO is able to run several copies of 
SHELXE simultaneusly (which can be more effective). On the other hand 
SHELXL, SHELXD and SHELXT (widely used to solve small molecule 
structures) are themselves highly parallel (and also distributed with CCP4).


George


On 11/23/2018 12:30 PM, Thomas, Jens wrote:

PHASER and SHELXE can take advantage of multiple CPUs, as can most of the 
Molecular Replacement pipelines such as AMPLE and ARCIMBOLDO.

It does depend on whether all the CPUs have access to shared memory, though. If 
the program is parallellised with threads (such as SHELXE for example), 
exploiting multiple CPUS would require that all the CPUS have access to shared 
memory.

Best wishes,

Jens

From: CCP4 bulletin board  on behalf of Harry 
Powell<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: 23 November 2018 11:05:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] buying a cluster

Hi

For X-ray diffraction image processing, both XDS and DIALS can use multi cpus.

For cryo-EM, Relion can run on multi-cpus, but can also make good use of GPUs, so don't 
forget this as an option if you're going over to the "dark side"...

On 23 Nov 2018, at 10:30, V F wrote:


Dear all,
Which programs benefit from multi-cpu cluster? Since the physics
department is getting rid of a old 32 compute node cluster, I was
hoping to find some benefit using for crystallographic work. Looking a
ccp4wiki or google-fu did not help
Many thanks
Veronica



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University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312



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[ccp4bb] postdoc position for crystallographic methods development

[George Sheldrick]

In a couple of months time I expect to have funding for a postdoctoral 
position. The successful candidate would be expected to work with me in 
Goettingen on computational crystallographic methods development and 
provide support for shelx users, e.g. at workshops. Fluency in spoken 
and written english and either Fortran or Python as well as shelx 
experience would be highly desirable. One potential project would be to 
improve the program shelxd that is useful both for solving large equal 
atom small molecule structures and for locating anomalously scattering 
atoms in macromolecules, e.g. for sulphur-SAD phasing. Although shelxd 
is still used it has not been changed for decades and needs to be 
brought up to date. Anyone interested should contact me by email.


George Sheldrick

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry
University of Goettingen
Tammannstr.  4s due for a rewrite
D37077 Goettingen
Germany
Tel: +49 551 3933021 or +49 5594 227312



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Re: [ccp4bb] Combining MR and SIR phases

[George Sheldrick]

I'm afraid that I have to disagree with Eleanor, a very rare event. Both 
pure SIR and pure SAD give you only half of the necessary phase 
information. The initial map will in both cases be a double image. One 
then tries to improve it by density modification. For pure SAD one image 
is positive and one is negative, so just setting negative density to 
zero is a good start. For pure SIR both images are positive so this does 
not help, the map remains centrosymmetric. This also explains why SAD 
works much better if the solvent content is high, there is less danger 
of the images canceling each other. This is much less of a problem for 
MAD or SiRAS, both of which could work for a bromine derivative. If you 
collected Friedel opposites you may still be able to try SIRAS.


George


On 23.07.19 11:43, Eleanor Dodson wrote:
Well - there are lots of ways to proceed. It doesnt really matter for 
the crystallography theory if the exptl phases are from SAD or SIR. 
Just harder to handle in some software
I think I would start to refine the poor MR model with the xptl phases 
as restraints.
REFMAC will do this. Then see if the maps look better - can you see 
features not in the model?..
If they do you could use Buccaneer to try to rebuild the existing 
model using exptl phases..

It might work!
Eleanor

On Tue, 23 Jul 2019 at 09:55, Luke Smithers 
> wrote:


Hi all,

I have collected native data and data on a bromide derivative of
one of my crystals, but have struggled to get a second derivative.
I went through the SIR pipeline as the anomalous signal from the
Br was weak and have generated some not-so-great phases. I have
also attempted MR with the closest match in the PDB (which is only
22% sequence identity) and got some more not-so-great phases. I
have found plenty of programs that will combine SAD/MR phases, is
there anything that will do SIR/MR? I understand it's likely I
will need more and better data and ideally a second derivative but
thought it was worth putting it out there to see if there is
something like this.

Luke

-- 


*Luke Smithers*

*PhD Candidate*

Protein Production and Structure Facility, School of Molecular
Sciences

*T *+61 8 6488 3163

The University of Western Australia





Pursue Impossible

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Dept. Structural Chemistry
University of Goettingen
Tammannstr.  4
D37077 Goettingen
Germany
Tel: +49 551 3933021 or +49 5594 227312




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Re: [ccp4bb] Shelx and debian 10

[George Sheldrick]

As explained in the attached email from Peter Keller, I was deliberately 
preparing the binary Linux SHELX distribution using older (2011) system 
libraries so that the programs would run on older systems that many 
users are still using. Unfortunately this means that they do not run on 
some recent cutting edge distributions including Debian 10. This can be 
fixed with 'vsyscall=emulate' when installing the OS but not all users 
may be allowed to do this. Dynamic binaries would be smaller but would 
require the user to provide the right libraries.


If I prepare statically linked binaries (using the latest ifort and 
ubuntu) they appear to run on current systems but may have problems on 
older systems. I may have to offer (e.g. in CCP4 and on the SHELX 
server) two sets of Linux binaries in the future, one for 'vintage' 
systems and one for current systems. Alternatively I could provide both 
statically and dynamically linked versions. What do users think?


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:
. 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 

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 – 

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

[George Sheldrick]

Dear Matthias,


That is very strange. First please repeat the shelxl refinement with the 
occupancy of the offending chlorine(s) in the .ins file changed from 11  
(i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If 
that does not help I would be happy to look at it in confidence, I would 
need the .hkl and .ins files.



Best wishes, George




On 03.02.20 12:08, Barone, Matthias wrote:


Dear ccp4 community

Im having some problems solving a 0.73A structure. Spacegroup seems to 
be correct, data are not twinned, 95.5% overall completeness, ISa 
25.6. Outer shell CC1/2 24% and 90.4% complete.


The model is nearly fully built, there is no remaining unmodelled 
areas. However, Rfact isstuck 27% in phenix, with a very distinct 
artifact in the electron map (see phenix.jpg). You can see difference 
density on various well defined sidechain atoms. Notably, they seem to 
follow a pattern: Nearly all Val CG have difference signal, as well as 
many backbone NH. Hence, I suspected that it might be a problem with 
the SF, since we recorded the DS at 0.86A.



Hence I gave shelxl a shot:

I used the refined model from phenix, converted it via pdb2ins and 
pasted the restraints created by prodrg.


The shelxl hkl was produced by xdsconv, using the freeR flagging of 
the mtz used by phenix (no merge, friedel false).


Interestingly, shelxl can bring Rfree down to 16% and almost all of 
the diff-density artifacts seen before are 
gone (shelxl_noSFAC-CL.jpg). Except one: the inhibitor contains a 
chlorinated phenylring (pdb ligand 2L5) which now shows massive 
difference density for Cl.


I therefore suggested that I might deal with a wrong SF for Cl. Funny 
enough, pdb2ins does not produce a DISP line for Cl if converting the 
pdb that 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 $CL    0.18845    0.21747   1035.16450

into the .res file andupdated 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




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Tammannstr.  4
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Re: [ccp4bb] Question about P3, H3 and R3 space groups

[George Sheldrick]

This is precisely why SHELX always used the coordinates of the general 
position (LATT+SYMM) to define the space group rather than a name or number.


George

On 22/07/20 14:15, Ian Tickle wrote:


Hi David

The problem is that the PDB incorrectly used the H lattice symbol 
(without consulting any crystallographers AFAIK) for the hexagonal 
R-centred cell when it had already been in use for many years for the 
triply-primitive setting of P3, so now we have this confusion between 
MX & XRD/powder usage. It's probably now too late to do anything about 
it.  Simply put: in XRD/powder software H3 is #143 as originally 
specified in IUCr Int. Tab.; in MX software H3 is #146.


What should have been used are the Hermann-Mauguin symbols for the two 
R3 cells: R3:r and R3:h (see the syminfo.lib file).


This is a constant confusion between the standard symbol (i.e. one of 
the 230 space-groups in their standard settings) and the setting 
symbols.  Other common examples are space group #5 with standard 
symbol C2 which has a number of alternative settings A121, B112, C121, 
I121 etc., and standard symbol P21212 with settings P22121, P21221 and 
P21212, all of which are equally valid.  The conventional IUCr choice 
of setting is determined by the relative cell lengths (as far as 
possible c >= b >= a) and the cell angle (which in monoclinic cells 
should always be chosen >= 90 and closest to 90).  In practical 
crystallography it's the setting symbol that matters; the standard 
symbol is relevant only for classification, so in practice only the 
setting symbols should be used/


Cheers

--  Ian


On Wed, 22 Jul 2020 at 12:32, David Vizarraga Revuelto 
mailto:dvr...@ibmb.csic.es>> wrote:


Dear all,

Let me ask a question about the P3,H3, R3 space group annotations.
I had the idea that H3 was the recommended annotation for the
hexagonal representation of R3 (space group number 146). However,
in the Birbeck space groups web page (attached) H3 is associated
with the space group number 143 corresponding to P3. Similarly for
all the other H groups assigned in the page. Moreover in the
web page none of the R space groups is assigned to an H annotation.

H3 corresponds to 143 or  to 146?
Is there a space group 154 annotated as H32 1 2?

Many thanks.



"Note that the figure showing the relationship between primitive
and R-centred rhomohedral cells with hexagonal axes is clickable

Rhombohedral with Hexagonal axes
146. /R/ 3    148.
/R/ -3    155.
/R/ 3 2   160.
/R/ 3 /m/ 161.
/R/ 3 /c/ 166.
/R/ -3 /m/ 
167. /R/ -3 /c/ 
  
H-centred Trigonal
143. /H/ 3    144.
/H/ 3_1   145.
/H/ 3_2   147.
/H/ -3    149.
/H/ 3 2 1 150.
/H/ 3 1 2 
151. /H/ 3_1  2 1 
152. /H/ 3_1  1 2
  153. /H/ 3_2  2
1 154. /H/ 3_2
 1 2  156. /H/ 3
1 /m/ 157. /H/ 3
/m/ 1 
158. /H/ 3 1 /c/ 
159. /H/ 3 /c/ 1 
162. /H/ -3 /m/ 1 
163. /H/ -3 /c/ 1
  164. /H/ -3 1
/m/   165.
/H/ -3 1 /c/ 




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This message was 

Re: [ccp4bb] biomolecular NMR for IDPs

[George Sheldrick]

As Joel has suggested before, alphafold on an IDP would be interesting 
and would seem like a zero-cost starting point - perhaps one you have 
tried already.




Sent from ProtonMail mobile



 Original Message 
On 15 Aug 2021, 15:53, Scott Horowitz < scott.horow...@du.edu> wrote:


   Hi Sorin,

   I hate to say it, but this is a really tough and expensive one.
   Solving a true conformational ensemble of one IDP of decent size
   (~>70 residues) at something like decent resolution is hard, and not
   that many labs actually do it (it's usually a different set of NMR
   techniques than solving folding proteins, and that knowledge is even
   somewhat specialized even within the NMR community). Solving a
   co-structural ensemble of two IDPs that bind is even harder, and I'm
   hard pressed to remember a single case right now where it's been
   done (probably has, but very rarely). Assuming they express really
   well and produce decent spectra, it is in theory doable, but I'd
   assume multiple years of work by a very good student or postdoc from
   a lab that specializes in this and many thousands of dollars (I'd
   very roughly assume ~$10k in materials costs alone) would be
   required for that co-structure.

   The SAXS route is certainly less expensive and faster if it works
   and gets you the info you need, but it certainly will be low-res.
   I'm not as familiar with it, but if you can differentially label the
   proteins, the neutron equivalent of SAXS might also help with the
   co-structural ensemble to differentiate which protein is where in
   the resulting blob.

   Scott

   Scott Horowitz, Ph.D.

   Assistant Professor

   Department of Chemistry & Biochemistry

   Knoebel Institute for Healthy Aging

   University of Denver

   ECS Building

   2155 E. Wesley Ave

   Denver, CO 80208

   Phone: 303-871-4326

   Fax: 303-871-7915

   Zoom Room: https://udenver.zoom.us/my/scotthorowitz
   **

   Email: scott.horow...@du.edu

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   *From:* CCP4 bulletin board  on behalf of
   Roopa Thapar <070a21fba45f-dmarc-requ...@jiscmail.ac.uk>
   *Sent:* Sunday, August 15, 2021 8:20 AM
   *To:* CCP4BB@JISCMAIL.AC.UK 
   *Subject:* [EXTERNAL] Re: [ccp4bb] biomolecular NMR for IDPs
   [External Email From]: *owner-ccp...@jiscmail.ac.uk*



   Hello Sorin,


   1. The cost of getting NMR data on the IDPs you propose depends upon
   the expression levels of the protein/s as you will need to label
   with 15N and 13C - and depending upon your overall yields per liter
   of E.coli culture, this can add up.  In addition you will need to
   run triple resonance experiments - so you should look into the
   hourly charge to access the NMR spectrometers where you are
   located.  Moreover, you need to account for time required for
   optimization of solution conditions to collect the NMR data as the
   sample needs to be homogenous (as in no aggregation) at millimolar
   or hundreds of micromolar concentration.   As Ethan Merritt
   suggested, it would be a good idea to use SAXS first as it requires
   very little sample, no isotope labeling, and you can try to narrow
   down the solution conditions that would be best suited for NMR. The
   Kratky plots, Rg values under different solution conditions can give
   very useful information about conformational states and ensembles
   populated by IDPs. However, although NMR tends to be more expensive
   than other techniques but is perfect for IDPs as you point out you
   can get residue specific information.  A combined NMR/SAXS approach
   has proven to be very useful to validate computational models.

   2. In general, CROs are much more expensive particularly for
   generating isotopically labeled samples - it is cost-prohibitive for
   academic labs.  Genscript is one CRO that will express proteins, but
   I am not sure if they will make isotopically labeled proteins for NMR.

   3. The amount of protein needed depends upon the size of the
   molecule.  You will need at least 2-3 samples that are
   differentially labeled with 15N, 13C (also since you want data on
   the free and bound forms of the complex) at 0.5 - 1 mM depending
   upon the size of the molecule which relates to the complexity of the
   NMR spectrum due to number of resonances and the relaxation times. 
   The total volume required for each sample is between 280 ul - 600
   ul, depending upon which type of instrumentation and NMR probes you
   have access to.

   Hope this helps!

   Best regards,
   Roopa

   On Saturday, August 14, 2021, 04:12:58 PM CDT, Sorin Draga
wrote:


   Hello everyone,

   I do realize that this is not a NMR focused group, but I do hope
   that there are a few spectroscopists lurking around that could
   possibly answer a few questions (I am more of a
   modeler/computationalist):

   The