Re: [ccp4bb] Comparing two datasets

[LEGRAND Pierre]

Hello Mirek, 

A very quick approach for that is offered by pointless: 

pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz 
or 
pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK 

You will obtain a table looking like that, taking into account to possible 
reindexing: 

Alternative indexing scores relative to reference 
Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation 
1 [h,k,l] 0.993 0.962 0.118 19150 0.08 
2 [-k,h,l] 0.007 0.078 0.512 19150 0.87 


Best wishes, 

Pierre Legrand 
PROXIMA-1 Beamline 
Synchrotron SOLEIL 


De: "Nicolas Foos"  
À: CCP4BB@JISCMAIL.AC.UK 
Envoyé: Mardi 26 Juillet 2022 08:36:35 
Objet: Re: [ccp4bb] Comparing two datasets 



Hi Mirek, 


I am pretty sure XSCALE will do that for you : [ 
https://xds.mr.mpg.de/html_doc/xscale_program.html | 
https://xds.mr.mpg.de/html_doc/xscale_program.html ] 


If not, maybe have a look on SHELXC in SIR mode. 


Hope this help. 


Nicolas 
On 25/07/2022 21:52, Cygler, Miroslaw wrote: 


Hi, 
I would like to calculate the R-merge for Fs from two datasets processed from 
two different crystals. Tried to use Blend but got the message that Blend 
requires R. Downloaded R but do not know how to tell CCP4 where it is located 
on my Mac. Is there another program that would take two mtg files and merge the 
Fs? 
Any help would be greatly appreciated. 
Mirek 








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-- 
Nicolas Foos PhD - ARISE fellow [ https://orcid.org/-0003-2331-8399 | 
https://orcid.org/-0003-2331-8399 ] EMBL Grenoble, McCarthy Team
71 av. des Martyrs, 
38000 Grenoble FRANCE
   
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Re: [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

[LEGRAND Pierre]

Dear Vito,
In that case, and from what I can see from the picture you shared, I would 
guess that it is mainly the effect of the low occupancy of this I3C. The peak 
height of the iodide atoms seems low.
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito Calderone 
[calder...@cerm.unifi.it]
Envoyé : mercredi 10 juin 2020 10:54
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

Dear John,
   I would say that in that case the FoFc is basically flat.

Vito

Da: CCP4 bulletin board  Per conto di John R Helliwell
Inviato: mercoledì 10 giugno 2020 10:40
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

Dear Vito,
The I3C isn't like the platins as a challenge to the 2Fo-Fc map.
It maybe is more akin to the situation we described here:-
https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219
ie what does your Fo-Fc map, with three iodines placed, at the correct 
occupancy, look like?
Best wishes,
John
Emeritus Professor John R Helliwell DSc




On 10 Jun 2020, at 09:34, Vito Calderone 
mailto:calder...@cerm.unifi.it>> wrote:
Dear Pierre,
I was in particular talking of 2FoFc refinement maps.
In the attached picture for example you can see the 2FoFc map contoured at 1
sigma level of an I3C molecule bound to a protein where for I3C the only
visible density is that of iodines whereas the density of the other atoms of
the ligand is insignificant.
Best regards

Vito

-Messaggio originale-
Da: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Per conto di LEGRAND Pierre
Inviato: mercoledì 10 giugno 2020 09:31
A: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density

Dear Vito,
Could you precise in what kind of maps are you experiencing these effects:
2FoFc refinement maps or experimental phasing ?
I had this kind of effects long ago in experiemental phasing due to Fourier
transform ripple effects. This could be due to scaling problems, low
resolution truncation or incompletness (maybe intensity overloads).
Another source condition could be local X-ray dose degradation due to the
high absoption of the metals.
Best regards,
Pierre Legrand
PROXIMA-1, SOLEIL

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
Calderone [calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Objet : [ccp4bb] Heavy atom 
vs light atoms density

Dear All,
  many of us have probably experienced that, in the diffraction
of protein ligands containing heavy atoms (cisPt, I3C, etc), the
overwhelming electron density of the metal can totally flatten that of the
light atoms around (or rather make it look insignificant).
Is anyone aware of an article/review (to use as a reference) in which this
is clearly stated/pointed out?
Best regards

Vito Calderone





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Re: [ccp4bb] Heavy atom vs light atoms density

[LEGRAND Pierre]

Dear Vito,
Could you precise in what kind of maps are you experiencing these effects: 
2FoFc refinement maps or experimental phasing ?
I had this kind of effects long ago in experiemental phasing due to Fourier 
transform ripple effects. This could be due to scaling problems, low resolution 
truncation or incompletness (maybe intensity overloads).
Another source condition could be local X-ray dose degradation due to the high 
absoption of the metals.
Best regards,
Pierre Legrand
PROXIMA-1, SOLEIL

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito Calderone 
[calder...@cerm.unifi.it]
Envoyé : mercredi 10 juin 2020 08:42
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Heavy atom vs light atoms density

Dear All,
   many of us have probably experienced that, in the diffraction of 
protein ligands containing heavy atoms (cisPt, I3C, etc), the overwhelming 
electron density of the metal can totally flatten that of the light atoms 
around (or rather make it look insignificant).
Is anyone aware of an article/review (to use as a reference) in which this is 
clearly stated/pointed out?
Best regards

Vito Calderone





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Re: [ccp4bb] Interesting pattern on a crystallization drop

[LEGRAND Pierre]

Dear Beatriz,

Nice drops :-))
Could it be that there is a reaction going on in these drops ?
The conditions are quite "exotic" with possibilities of coordination or 
oxydoreduction (Co2+/Co3+) or polymerization...
Do you have reductants with the protein buffer ?
Is the protein an enzyme or a metalloprotein ?
Just some ideas.

Best wishes,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Beatriz Gomes 
Guimaraes [beatriz.guimar...@fiocruz.br]
Envoyé : mercredi 27 mars 2019 19:44
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Interesting pattern on a crystallization drop


Dear all,


I would like to share with you a surprising pattern I found when examining some 
crystallization plates (attached figures).


It is less obvious looking the photos, but apparently the "lines" are formed by 
precipitated protein and there are some "bubbles" with small drops inside. I 
wish they were microcrystals but I do not think this is the case.

I was suprised by the symmetry !


And it is not completely random because for the same condition the difference 
between the two drops are : protein alone ("hexagon") and protein + ligand 
("rhombus")


crystallization condition is:

0.01 M Cobalt(II) chloride hexahydrate

0.1 M Tris pH 8.5

20% w/v Polyvinylpyrrolidone K 15


Have you seen anything similar before?


Thank you for your comments!

Beatriz



--
Beatriz Guimarães
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ Paraná
Rua Prof. Algacyr Munhoz Mader, 3775   Bloco C
CIC 81350-010
Curitiba - PR, Brasil
Tel.:+55(41)3316-3225/2104-3438



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Re: [ccp4bb] Racemic crystallography and structure solving problem

[LEGRAND Pierre]

Hi Prasum,

In such case, with xia2 you could try to add the option: small_molecule=true.
This will enable the consideration of centrosymmetric spacegourps.
Or you can try in pointless the options:
CHIRALITY  NONCHIRAL or CENTROSYMMETRIC

Your spacegroup could be P-1 (#2).
Good luck,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Prasun Kumar 
[prasun.ku...@bristol.ac.uk]
Envoyé : lundi 4 mars 2019 16:33
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Racemic crystallography and structure solving problem

Hi All:

I have performed racemic crystallography and got crystals that diffracted. The 
automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives 
the space group as P1 and cell dimension
42.78   52.16   54.49   114.11  92.16   92.31.

Challanges start from here:

1) How much I should be assured of the space group as I expect my peptides to 
get crystallized in the same group, but by default we get the same space group.
2) Is there any seperate method for processing the raw images in my case.

I used the merged .mtz file for phasing. However, I always get the warning that 
eLLG score is low and it is difficult to fit a single copy of the ensemble. 
CC1/2 and I/SigI are in acceptable range. Completeness is also more than 95%.

My peptides, 30 residues long, form an oligomer. However, I do not have 
reliable model of oligomers to start with. I have taken a single helix of 
length 24, 12 and 6 residues to phase, but no luck so far.
Any guidelines will be really helpful.

I am happy to provide any other relevant information, if one wants.

Thanx in advance
Prasun



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Re: [ccp4bb] Iron Oxidising state

[LEGRAND Pierre]

Hi,

Due to the absorbed X-ray dose and photoreduction process during 
datacollection, it is most probably Fe+2. See for example:
J Biol Chem. 2013 Apr 
5; 288(14): 9648–9661.
 doi:  10.1074/jbc.M112.438796
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617268/

Bests,
Pierre Legrand
PROXIMA-1 synchrotron-SOLEIL


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de rohit kumar 
[rohit...@gmail.com]
Envoyé : vendredi 5 janvier 2018 11:45
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Iron Oxidising state

Dear All,

I am solving a structure (resolution 2 A) of an enzyme having Iron as a metal 
cofactor.

How could I know oxidising state of the bound Iron (Fe+2 or Fe+3)?


Thank you in advance


--
WITH REGARDS
Dr. Rohit Kumar Singh

Re: [ccp4bb] new ContaMiner features

[LEGRAND Pierre]

Dear Gérard,

As being part of the group how has initially raised the issue to Stefan, I 
stand out to try clarifying a misinterpretation.
In brief, because we are happy users of StarAniso, it happened that we have 
submitted an mtz that it had produced to the ContaMiner server. We were very 
surprised to find that almost all contaminants evaluated gave high scores 
according to MoRDa. On the contrary, using an "isotropicaly" treated mtz, no 
hit could be detected in by ContaMiner.

Being collected on PROXIMA-1 beamline, it coun't be a "badly collected 
datasets" ;-)

So, most probably, as you suggested, the issue is linked to some bad 
assumptions made by MoRDa or inadequate criteria choices _in_the_cases_ of 
"corrected" anisotropic data. 
We can probably provide some examples of datasets to the developers willing to 
pursue investigations on this.

I completely agree with Tristan! I have to admit having lost several weeks in 
my career (if not months) with "contaminated" crystals. And working on an MX 
beamline, I can testify that this is unfortunately happening regularly. 

I will finish with a big thanks to all the (StarAniso/ContaMiner/MoRDA) 
developers how are helping us to untwist the unavoidable experimental 
mess/reality.

Kind regards,
Pierre 

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Gerard Bricogne 
[g...@globalphasing.com]
Envoyé : jeudi 23 novembre 2017 19:34
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] new ContaMiner features

Dear Stefan,

 Regarding your final paragraph: your server carries a warning
with the exact wording:

 "Submitting StarAniso files can give you suspicious results. Use
with care!"

 It seems rather regrettable that you are posting such a public
warning without ever having contacted the STARANISO developers about
your observations, nor giving any information about what you call
"suspicious" or what the "care" you recommend would consist of.

 We have taken a great deal of care ourselves in developing the
program and offering it to the community through a server, and the
least we would have expected is that any pattern of "suspicious"
results would be referred to us so that we could investigate them.
There may be some assumptions made in MoRDa that we are not aware of,
that might be incompatible with assumptions made in STARANISO - who
knows? Or it could be that some particularly badly collected datasets
are made to look worse after their anisotropy analysis.

 Could we discuss your observations, and what it is exactly that
you call "suspicious", before they end up being referred to in such an
uninformative manner as some sort of "Government Health Warning"?

 I think that would be nice :-) and we would be only too keen to
take whatever extra "care" is needed ourselves. We would all learn
something.


 With best wishes,

  Gerard.

(on behalf of the STARANISO developers)

--
On Thu, Nov 23, 2017 at 05:02:39PM +0100, Stefan Arold wrote:
> Dear Community,
>
> A quick message to announce the following two new features on our
> ContaMiner web server for the automated detection of unwantedly
> crystallised contaminants (
> https://strube.cbrc.kaust.edu.sa/contaminer/submit)
>
> 1) online visualisation of 2FoFc and FoFc maps. In cases of positive
> results, the ‘UglyMol’ tab allows to inspect 2FoFc and FoFc maps directly
> in the web browser. Thi
>
> 2) life-update. Previously, results were sent to you once all ~2000 MR jobs
> were finished. Now, the individual results for each potential contaminant
> will appear as soon as they are finished. This feature should substantially
> shorten the time for identifying positive results (i.e. contaminant
> detected), which are terminated faster than negative ones.
>
> 3) custom contaminants. In the ‘Advanced’ tab, users can upload own PDB
> files (more than one is possible) to be included as search models. This
> feature can be used to include PDB files from your lab bench neighbour’s
> project to test for potential lab internal contaminations (through
> bacterial contamination or through mix-up of plasmids or glycerol stocks).
> This feature could also be ‘abused’ as a means to use the MoRDa pipeline to
> run molecular replacements with template structures that are not yet
> deposited in the PDB; for example to run molecular replacement and initial
> refinement for liganded or complexed versions of an unpublished structure.
> This might be particularly interesting for crystallographers away from
> their usual home software environment (e.g. at the beamline).
>
> Finally, a word of warning – Staraniso files might give false positives if
> they have large anisotropic cuts.
>
> Keep your crystals clean!
>
> With best wishes
>
> The ContaMiner Team

--

 ===
 * *
 * Gerard Bricogne 

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

[LEGRAND Pierre]

It seems to me important here to remind that this wave-particle duality is not 
limited to photons. Electrons and neutrons of course, but also atoms and even 
molecules have to be considered. To illustrate this, and since it is Friday, 
shall I propose some nice reading for the week-end :

Wave-particle duality of C60
Markus Arndt , Olaf Nairz, Julian Voss-Andreae, Claudia Keller,Gerbrand 
van der Zouw, 
and Anton Zeilinger
Nature 401, 680-682, 14.October 1999

See also: from the same group:
http://130.58.92.210/Students/phys%205_2010/zeilinger%20ajp%202003.pdf
https://www.univie.ac.at/qfp/research/matterwave/c60/

Have a nice weekend,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp 
[b...@ruppweb.org]
Envoyé : vendredi 22 mai 2015 09:13
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] X-rays and matter (the particle-wave picture)

Hi Fellows,

Zbi's response has addressed refs and the technical complexities that arise
when describing
the scattering process on a microscopic QM basis.

I shall tell you why I decided to provide this probabilistic QM
interpretation.

First, a probabilistic approach to empirical science is the overarching
theme of the book.
Examples range from Bayes to ML and necessarily, the interpretation of
quantum mechanics.

Having been tortured in Vienna as experimental physicist with instruments
that Boltzmann built
and probably already Schrödinger broke, when I saw for the first time these
explanations
of Bragg's equation (footnote *) where 2 incoming, interfering waves are
pictured,
I was confused. Can't be.

The first fact to drive across is that there is no coherence between the
photons emitted
from a conventional source (and under normal operations with exceptions and
caveats
I am not going into, also from synchrotrons):
In demonstrations with a laser and a diffraction slide, invariably a
fraction of students exposed to
these Bragg drawings seem to erroneously but justifiably assume that the
coherence
of the laser is relevant to diffraction.
It is the monochromaticity and the brilliance of the laser that makes the
experiment work
so well, not any necessity for coherence between incoming photons.
This is why I avoided throughout the book to show illustrations with 2
incoming
waves or wave vectors, as observant readers may have noticed.

Second, as a fundamental principle, a macroscopic phenomenon based on the
average
of many microscopic processes taking place on a quantum mechanical scale can
often
be well explained with a 'classical' picture. That is why this partial wave
recombination
business for structure factors works.

For me a more logical and consistent approach is to treat diffraction as a
probabilistic
phenomenon, with the underlying probability distribution simply given by the

structure factors. Also the square proportionality between |F| and I follows
naturally
from quantum mechanics as the observable of these complex probability
functions.
So, this quantum mechanical interpretation (note the word interpretation) is
very
consistent and imho unforced and almost beautiful. But, as noted, the
underlying microscopic
process description is less than trivial, and defies our macroscopic
experience. And
beauty is in the eye of the beholder

Historically, of course, when the first diffraction images were taken and
the Braggs
began to make sense of the images, QM was in its infancy. The ultraviolet
catastrophe
was fresh in the minds, and the photoelectric effect published only in 1905.
The Bohr model
came out in 1913, and it took about another  10+ years for Heisenberg,
Schroedinger
 Cie. to come up with workable theories. So, the Braggs are excused, but
today I think
a more modern picture involving the underlying QM picture can be presented.
*

If you are interested in the philosophical issues w/o becoming a quantum
physicist, there are
interesting accounts about the early history of quantum mechanics which I
find a most
fascinating period in physics. I can provide a few refs off board later when
I am back at my library.

So, yes I am guilty of not providing a more concise intro to QM, but as
Dirty Harrys says:
'Man's gotta know his limits'

Best, BR

* [The brilliance of the Bragg equation imho is to combine the 3 independent
Laue equations
(unhandy) by simply turning the Laue 'pictures' so that reflection on
lattice planes - much
more intuitive - can be used to relate the diffraction angle (nota bene, not
the direction
anymore) to lattice spacings.]

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Zbyszek Otwinowski
Sent: Friday, May 22, 2015 4:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] X-rays and matter (the particle-wave picture)

The answer to your questions depends on the level of understanding of
quantum mechanics. I am sending info where to find the subject discussed in
more details.

Bernhard Rupp's 

Re: [ccp4bb] self-rotation in the absence of NCS

[LEGRAND Pierre]

Hi Peer,

The first thing I would suggest is calculating the self-rotation again but 
using the FC from the refined model, for comparaison. Then, if you don't see 
the same supplementary peaks, you can try to play with the integration radius 
and resolution range. This could give you some hint on the origin of these 
peaks.

Best regards,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Peer Mittl 
[mi...@bioc.uzh.ch]
Envoyé : mercredi 29 avril 2015 13:59
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] self-rotation in the absence of NCS

We are working with a multi-domain protein crystallized in SG P6_5 with
one molecule per asymmetric unit. The structure was refined at 2.00 A
resolution with reasonable R-factors but unfortunately the domain we are
most interested in seems to be disordered. Interestingly, the
self-rotation function shows peaks on the kappa=180° plane (omega=90°,
phi=19° (and every 30°)), with more than 50% origin peak height.
Therefore, we are wondering if perhaps the space group assignment might
be sub-optimal. Any explanations how these self-rotation peaks could
occur and how we could extract meaningful information to resolve the
disordered domain are welcome.

Best regards,
Peer

P.S. Some additional information: pointless suggests SG P6_5, the data
doesn't seem to be twinned (L-test), the refined part of the structure
has no internal symmetry and refinement in P1 doesn't reveal the
lost domain.

--

Peer Mittl, PD Dr.
Biochemisches Institut
Universität Zürich
Room 44M03
Winterthurer Strasse 190
CH-8057 Zürich

Tel.   +41-(0)44-6356559
Mobile +41-(0)76-2776566
Fax.   +41-(0)44-6356834
Mail   mi...@bioc.uzh.ch

[ccp4bb] Probleme with D-peptide cif dictionary with refmac5.8

[LEGRAND Pierre]

Dear all,

A quick note to report the problems I have experienced (and a solution) with 
the refinement of a peptide containing both D- and L-amino-acids with refmac5.8 
(Refmac_5.8.0073).
This refinement was done with high resolution data, with hydrogens included in 
the model (important to remember !).

When using the standard dictionary for D-TRYPTOPHAN: $CLIBD_MON/d/DTR.cif, most 
of the geometrical definitions were altered after the inserted D-amino-acid. 
The geometrical Rms deviations are strongly increased already at the first 
cycle (see differences of two runs at the end of my message). 

The first solution was to generate a new cif dictionary from the standard 
TRP.cif file in the following way:

sed -e 's/negativ/positiv/'  -e 's/TRP/DTR/g' -e 's/L-peptide/D-peptide/' 
$CLIBD_MON/t/TRP.cif   DTRP.cif

Running again refmac5 with this cif file using the LIBIN DTRP.cif instruction 
produced the more sensible results. 

It looked to me that the TRP and DTR cif definitions have diverged at some 
point. Looking more closely at the differences in this two files, pointed me to 
this:
Hydrogen on the indole NE1 is named HE1 in TRP and HNE1 for DRT...
Using a pdb file with HE1 renamed as HNE1 worked with the current DRT file, but 
with slightly worst results.

The DTR.cif file probably needs to be updated (and maybe the other 
D-amino-acids cifs also revisited).

Best regards,
Pierre

PS1. I can send the log and pdb files to developers if they are interested.
PS2. I haven't checked with other D-amino-acids, since I have only this one in 
my structure.

With modified TRP as DTRP.cif:
  InitialFinal
R factor0.0865   0.0847
  R free0.0913   0.0896
  Rms BondLength0.0181   0.0175
   Rms BondAngle2.2555   2.2407
  Rms ChirVolume0.1131   0.1154

With standard DRT.cif file:
  InitialFinal
R factor0.0865   0.1916
  R free0.0913   0.2006
  Rms BondLength2.4522   1.7415
   Rms BondAngle   33.3672  32.1460
  Rms ChirVolume1.1972   1.0767

With DRT.cif and renamed HE1 as HNE1:
  InitialFinal
   R factor0.0865   0.0848
 R free0.0913   0.0901
 Rms BondLength0.0207   0.0200
  Rms BondAngle2.4024   2.3884
 Rms ChirVolume0.1122   0.1140

[ccp4bb] Call for beamtime on PROXIMA, FIP and SWING beamlines

[LEGRAND Pierre]

Dear all,

We would like to draw your attention that the deadline for SOLEIL's (and French 
ESRF-CRG) next call for proposal is approaching: September 15th, 2014 – 23:59 
(French time).

Four beamlines relevant for the MX community are accessible through the SUNSET 
online proposal system (http://sunset.synchrotron-soleil.fr/sun): PROXIMA1, 
PROXIMA2, FIP and SWING.

MX PROXIMA 1 Beamline (SOLEIL):
- Undulator beamline with flux of 1.4x10^12 photons/sec at 9 keV.
- Energy range: 5.8 to 16 keV (2.14 - 0.71 Å)
- Typical beam size: 45x25 microns
- Multi-axis Kappa gonimeter
- Detector: PILATUS 6M pixel array, 25 Hz frame rate.
- Sample changer: CATS robot with unipuck standard
- mxCuBE v2 acquisition software
- Well suited for large complexes.
http://www.synchrotron-soleil.fr/Recherche/LignesLumiere/PROXIMA1

MX PROXIMA 2 Beamline  (SOLEIL):
- Undulator beamline with flux of 1.4x10^12 photons/sec at 9 keV.
- Energy range: 6 to 15 keV (2.07 - 0.83 Å)
- Typical beam size: 10x5 microns
- MD2 single axis goniometer
- mxCuBE v2 acquisition software
- Detector: ADSC Q315r
- Sample changer: CATS robot with a large 9-unipuck dewar
- Well suited for selecting out sweet spots on heterogeneous crystals and 
finding micro-crystals
http://www.synchrotron-soleil.fr/Recherche/LignesLumiere/PROXIMA2

BioSAXS SWING beamline (SOLEIL):
- Undulator beamline with flux of 4x10^12 photons/sec at 12 keV.
- Energy range: 5 to 16 keV (2.48 - 0.71 Å)
- Typical beam size: 400x80 microns
- Online HPLC (Agilent), coupled to user-friendly SAXS control GUI
- Sample changer : Agilent injector module (2 x 54 vials)
- Detector: Aviex CCD 16 x 16 cm2, read-out time 200 ms
- Sample-To-Detector distance : from 1.1 to 6.6 m
- Data reduction : Soleil Foxtrot Software and US-Somo
- Data analysis : Atsas suite and Dadimodo
http://www.synchrotron-soleil.fr/Recherche/LignesLumiere/SWING

 MX FIP Beamline (BM30A, ESRF):
- Bending magnet beamline
- Energy range: 7 to 18 keV (1.77 - 0.69 Å)
- Detector: ADSC 315r
- Goniometer: MD2 (Maatel)
- Sample changer: CATS robot (soon: G-Rob double gripper sample changer)
- In-situ X-ray diffraction screening and data collection
- Soon: remote crystal harvesting
http://www.fip-bm30a.fr/
http://www.esrf.eu/home/UsersAndScience/Experiments/Beamlines/content/content/bm30a.html

Best regards,
Javier, Jean-Luc, Bill and Pierre

Re: [ccp4bb] pairwise CCano

[LEGRAND Pierre]

Hello Tim :-)

You can try to do this with sftools. It is also an interactive type of program 
input but you can easily calculate correlations. After converting xds files to 
mtz, you can try some thing like this : 

sftools  eof  sftools_1.log
READ $mtz1
READ $mtz2
SELECT RESOL  2.8
CORREL COL  5 10 SHELLS 10
eof

For the ploting, I'll use gnuplot after parsing the sftools_1.log file.
Good luck with this,
Cheers,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Envoyé : vendredi 14 mars 2014 10:33
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] pairwise CCano

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

I am looking for a tool that prints (and preferably plots, e.g. as
postscript) the pairwise anomalous CC vs. resolution for several input
HKL-files.
xprep does this, but it is interactive and requires a fair bit of
typing. Since I have a large number of HKL-files from XDS, I would like
to script that and then flip through the pages of the postscript-plots.

I looked into pointless but could not find even a table.

Since there recently were some publications one the use of many files
for phasing, I though such a tool should exist!?

Best,
Tim

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFTIszcUxlJ7aRr7hoRApYyAKDt36pF11DAbkfcXVq+uLjqvm91HgCfSZ+V
BVpiCx4q9DZZCqDLenHX374=
=itCO
-END PGP SIGNATURE-

[ccp4bb] RE : [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

[LEGRAND Pierre]

Hi,

Sorry, I'm a bit late on this one. 
I have just uploaded a new version of xdsme (0.5.0.2) that works with the 
latest version of xds. We have tested it for a few days on the beamlines, but 
do not hesitate to report bugs (directly to me).
You can catch it here: http://code.google.com/p/xdsme/
Cheers,

Pierre Legrand
PROXIMA1
Synchrotron SOLEIL

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Rain Field 
[rainfiel...@163.com]
Date d'envoi : mercredi 3 juillet 2013 10:20
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

Hi,
I found the current release of xia2 or XDSME is not compatible with latest XDS.
Is there any similar software available?
Thanks!

[ccp4bb] RE : [ccp4bb] Large unit cell, overlaps

[LEGRAND Pierre]

Hi Jason,

To answer your initial question about overlaps versus finer slicing, you can 
get a good description of the problem in Fig10 of Z. Dauter article 
Data-collection strategies  (open access article here: 
http://journals.iucr.org/d/issues/1999/10/00/ba0020/ba0020.pdf).

From the initial cell parameters, XDS calculates the Maximum oscillation range 
to prevent angular overlap at high resolution limit (bottom of the IDXREF.LP 
file). This calculation assumes zero mosaicity, and crystal in the worst 
orientation: with the longest axis perpendicular to the spindle axis.

You can easily have a finer estimation of this maximum oscillation by using the 
formula proposed in Zbigniew's article (bottom of page 1707). For example, 
using a very simple python script (attached) and the values you have given (and 
assuming a 0.1 degree beam divergence):

cell_parameters = 134, 151, 276, 90, 90, 90
mosaicity = 0.25
divergence = 0.1
results are:
  dmin a* b* c*
   4.02.06   1.87   1.18
   3.01.63   1.49   0.97
   2.01.21   1.11   0.77
   1.00.78   0.73   0.56

This shows that, in the worst orientation (c* perpendicular to the spindle) and 
the same mosaicity you could record up to 1A resolution data without overlaps 
using 0.56 degree oscillation range. In a better orientation, c* aligned along 
the spindle axis (using a kappa goniometer for example), you could use up to 
0.73 degree oscillations for the same high resolution.

In conclusion, since you have used 0.5˚ oscillations, if crystal moscaicity and 
beam divergence are correct, you shouldn't have overlaps problems.

TIPS1: Try using the refined diffraction parameters (cp GXPARM.XDS  XPARM.XDS) 
and profiles parameters (look for SUGGESTED VALUES in INTEGRATE.LP) to re-run 
xds using JOB=DEFPIX INTEGRATE CORRECT. You can repeat that several times if it 
improves integration statistics. 
TIPS2: Check that you don't have a pseudo-translational symmetry problem by 
calculating a native Patterson (or running phenix.xtriage)

Good luck,
Pierre

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Jason Busby 
[j.bu...@auckland.ac.nz]

Date d'envoi : mardi 17 juillet 2012 06:04

À : CCP4BB@JISCMAIL.AC.UK

Objet : Re: [ccp4bb] Large unit cell, overlaps





Hi,



Ok, IDXREF.LP shows that it was only using 1-262.  I tried running COLSPOT and 
IDXREF again, and it picks the same unit cell.



Pointless picks Pmmm and picks 2 definite screw axes, and one possible (p 
~0.5), so either P22121 or P212121.
I did change the number of grid points to 13 on my last integration run.
Distance seems to fluctuate from 303.7 to 298.7 - only 303 at the very 
beginning and then it drops down to 299 for the rest of the images.



At this point I'm mostly wanting to get a handle on what to do next time I'm 
collecting data - whether I need to collect finer slices or try and position 
the crystal in the loop at a different angle, or what.



Thanks for the help,



Jason.



--
Jason Busby
PhD Student
Laboratory of Structural Biology
School of Biological Sciences
University of Auckland
Thomas Building 110
3a Symonds St
Private Bag 92019
Auckland  1142
New Zealand



ph:  +64 9 3737599 ext 84155
fx:  +64 9 3737414




On 17/07/2012, at 3:44 PM, Bosch, Juergen wrote:


grep SPOT_RANGE IDXREF.LP should provide you information about that. No idea 
what the default would be.
How about pointless ?



Something else which might buy you a bit of signal is 





NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13



The default for both is 9, you'll end up with a finer profile 13x13x13.
If you grep for DISTANCE in INTEGRATE.LP is it stable ? If not you might want 
to define which values to refine in the integration step via 
INTEGRATE(REFINE)=CELL etc.



Jürgen




On Jul 16, 2012, at 11:28 PM, Jason Busby wrote:


Hi,



The autoindexing picks this unit cell pretty much unambiguously, and the 
profiles look reasonable.  These are crystals of a very large heterodimer (2177 
residues), and this unit cell would have 2 heterodimers and 56% solvent, which 
seems reasonable.  Scaling
 and merging produce reasonable statistics (I used aimless, not XSCALE):

   Overall  InnerShell  OuterShell
Low resolution limit   19.91 19.91  3.04
High resolution limit   2.99 16.38  2.99



Rmerge  (within I+/I-) 0.339 0.040 0.907
Rmerge  (all I+ and I-)0.348 0.045 0.949
Rmeas (within I+/I-)   0.360 0.042 0.994
Rmeas (all I+  I-)0.359 0.046 0.997
Rpim (within I+/I-)0.119 0.014 0.393
Rpim (all I+  I-) 0.085 0.012 0.291
Rmerge in top intensity bin0.053- - 
Total number of observations 1981569  5075 44784
Total 

[ccp4bb] RE : [ccp4bb] Large unit cell, overlaps [OOPS sign error]

[LEGRAND Pierre]

OOPS, I've made a big sign error in this simple calculation... Here are the 
more correct results, script and revised conclusion:

With the correct effect of mosaicity:
  dmin a* b* c*
   4.01.36   1.17   0.48
   3.00.93   0.79   0.27
   2.00.51   0.41   0.07
   1.00.08   0.03  -0.14

So, at your 3.A high resolution limit, you could already start to have overlap 
problems with 0.5˚ oscillation range, depending of c* orientation.
If you have 3-circle goniometer, try to orient c* along the spindle axis, 
otherwise use 0.25˚ oscillation range.

Pierre
 


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de LEGRAND Pierre
Date d'envoi : mardi 17 juillet 2012 08:26
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] RE : [ccp4bb] Large unit cell, overlaps

Hi Jason,

To answer your initial question about overlaps versus finer slicing, you can 
get a good description of the problem in Fig10 of Z. Dauter article 
Data-collection strategies  (open access article here: 
http://journals.iucr.org/d/issues/1999/10/00/ba0020/ba0020.pdf).

From the initial cell parameters, XDS calculates the Maximum oscillation range 
to prevent angular overlap at high resolution limit (bottom of the IDXREF.LP 
file). This calculation assumes zero mosaicity, and crystal in the worst 
orientation: with the longest axis perpendicular to the spindle axis.

You can easily have a finer estimation of this maximum oscillation by using the 
formula proposed in Zbigniew's article (bottom of page 1707). For example, 
using a very simple python script (attached) and the values you have given (and 
assuming a 0.1 degree beam divergence):

cell_parameters = 134, 151, 276, 90, 90, 90
mosaicity = 0.25
divergence = 0.1
results are:
  dmin a* b* c*
   4.02.06   1.87   1.18
   3.01.63   1.49   0.97
   2.01.21   1.11   0.77
   1.00.78   0.73   0.56

This shows that, in the worst orientation (c* perpendicular to the spindle) and 
the same mosaicity you could record up to 1A resolution data without overlaps 
using 0.56 degree oscillation range. In a better orientation, c* aligned along 
the spindle axis (using a kappa goniometer for example), you could use up to 
0.73 degree oscillations for the same high resolution.

In conclusion, since you have used 0.5˚ oscillations, if crystal moscaicity and 
beam divergence are correct, you shouldn't have overlaps problems.

TIPS1: Try using the refined diffraction parameters (cp GXPARM.XDS  XPARM.XDS) 
and profiles parameters (look for SUGGESTED VALUES in INTEGRATE.LP) to re-run 
xds using JOB=DEFPIX INTEGRATE CORRECT. You can repeat that several times if it 
improves integration statistics.
TIPS2: Check that you don't have a pseudo-translational symmetry problem by 
calculating a native Patterson (or running phenix.xtriage)

Good luck,
Pierre

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Jason Busby 
[j.bu...@auckland.ac.nz]

Date d'envoi : mardi 17 juillet 2012 06:04

À : CCP4BB@JISCMAIL.AC.UK

Objet : Re: [ccp4bb] Large unit cell, overlaps





Hi,



Ok, IDXREF.LP shows that it was only using 1-262.  I tried running COLSPOT and 
IDXREF again, and it picks the same unit cell.



Pointless picks Pmmm and picks 2 definite screw axes, and one possible (p 
~0.5), so either P22121 or P212121.
I did change the number of grid points to 13 on my last integration run.
Distance seems to fluctuate from 303.7 to 298.7 - only 303 at the very 
beginning and then it drops down to 299 for the rest of the images.



At this point I'm mostly wanting to get a handle on what to do next time I'm 
collecting data - whether I need to collect finer slices or try and position 
the crystal in the loop at a different angle, or what.



Thanks for the help,



Jason.



--
Jason Busby
PhD Student
Laboratory of Structural Biology
School of Biological Sciences
University of Auckland
Thomas Building 110
3a Symonds St
Private Bag 92019
Auckland  1142
New Zealand



ph:  +64 9 3737599 ext 84155
fx:  +64 9 3737414




On 17/07/2012, at 3:44 PM, Bosch, Juergen wrote:


grep SPOT_RANGE IDXREF.LP should provide you information about that. No idea 
what the default would be.
How about pointless ?



Something else which might buy you a bit of signal is





NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13



The default for both is 9, you'll end up with a finer profile 13x13x13.
If you grep for DISTANCE in INTEGRATE.LP is it stable ? If not you might want 
to define which values to refine in the integration step via 
INTEGRATE(REFINE)=CELL etc.



Jürgen




On Jul 16, 2012, at 11:28 PM, Jason Busby wrote:


Hi,



The autoindexing picks this unit cell pretty much unambiguously, and the 
profiles look reasonable.  These are crystals of a very large heterodimer (2177 
residues), and this unit cell would have 2 heterodimers and 56% solvent, which 
seems reasonable.  Scaling
 and merging

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

[LEGRAND Pierre]

Hi Kenneth,

I am experiencing exactly the same problem, in similar conditions: refinement 
with H at 0.84 A resolution.
From a bunch of tests made yesterday, I have found that it is linked to 
incompatibilities between   cif dictionaries definitions and H names in the 
input PDB.
For me, one simple solution to that problem, was to remove all H atoms from my 
input pdb and let refmac rebuild them (MAKE HYDR ALL).
I hope the trick will work for you.

By the way, I am facing an other problem: Clashes in inter residues H-bonds 
between H and acceptor atoms. What is the correct way to define these. The 
HYDBND pdb definition doesn't seems to work. Do I need to use LINK definitions 
? Is there a way to do that automatically ?

Cheers,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Robbie Joosten 
[robbie_joos...@hotmail.com]
Date d'envoi : vendredi 28 octobre 2011 09:42
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

Hi Kenneth,

This looks like an off-by-one bug in the restraint generation. Typical sources 
are weird LINKs, wrong atom names and bad luck. I suggest you make sure you 
have the very latest Refmac and dictionary and try setting up a new refinement 
instead of recycling an old job. If that doesn't work, we may need a closer 
look at your input model.

Cheers,
Robbie

 Date: Thu, 27 Oct 2011 20:48:49 -0500
 From: satys...@wisc.edu
 Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0
 To: CCP4BB@JISCMAIL.AC.UK

 Has anyone had problems with Refmac 5.6? I tried refining our stucture at 
 1.24 A,
 aniso with H in riding position and it just exploded! I get error in 
 distances such as

 Standard  External   All
 Bonds:  3270 0  3270
Angles:  4923 0  4923
   Chirals:   214 0   214
Planes:   368 0   368
  Torsions:   957 0   957
 ---

  Number of reflections in file  90428
  Number of reflections read  90428


  CGMAT cycle number =  1

  Bond distance outliers   
   

 Bond distance deviations from the ideal 10.000Sigma will be monitored

 A  5 PRO C   A - A  5 PRO HB1 A mod.= 3.344 id.= 1.329 dev= -2.015 
 sig.= 0.014
 A  5 PRO C   B - A  5 PRO HB1 B mod.= 2.997 id.= 1.329 dev= -1.668 
 sig.= 0.014
 A  5 PRO HB1 A - A  5 PRO HG1 A mod.= 2.292 id.= 1.458 dev= -0.834 
 sig.= 0.021
 A  5 PRO HB1 A - A  6 LEU HD23A mod.= 7.407 id.= 0.860 dev= -6.547 
 sig.= 0.020
 A  5 PRO HB1 B - A  5 PRO HG1 B mod.= 2.247 id.= 1.458 dev= -0.789 
 sig.= 0.021
 A  5 PRO HB1 B - A  6 LEU HD23B mod.= 6.529 id.= 0.860 dev= -5.669 
 sig.= 0.020
 A  5 PRO HG1 A - A  5 PRO HD1 A mod.= 2.267 id.= 0.980 dev= -1.287 
 sig.= 0.020
 A  5 PRO HG1 A - A  6 LEU N   A mod.= 4.860 id.= 1.530 dev= -3.330 
 sig.= 0.020
 A  5 PRO HG1 A - A  6 LEU HD21A mod.= 6.129 id.= 1.525 dev= -4.604 
 sig.= 0.021
 A  5 PRO HG1 B - A  5 PRO HD1 B mod.= 2.236 id.= 0.980 dev= -1.256 
 sig.= 0.020
 A  5 PRO HG1 B - A  6 LEU N   B mod.= 4.922 id.= 1.530 dev= -3.392 
 sig.= 0.020
 A  5 PRO HG1 B - A  6 LEU HD21B mod.= 6.664 id.= 1.525 dev= -5.139 
 sig.= 0.021
 A  6 LEU N   A - A  6 LEU CA  A mod.= 1.467 id.= 0.970 dev= -0.497 
 sig.= 0.020
 A  6 LEU N   A - A  6 LEU HA  A mod.= 2.005 id.= 0.970 dev= -1.035 
 sig.= 0.020
 A  6 LEU N   A - A  6 LEU CB  A mod.= 2.497 id.= 1.530 dev= -0.967 
 sig.= 0.020
 A  6 LEU N   B - A  6 LEU CA  B mod.= 1.469 id.= 0.970 dev= -0.499 
 sig.= 0.020
 A  6 LEU N   B - A  6 LEU HA  B mod.= 2.032 id.= 0.970 dev= -1.062 
 sig.= 0.020
 A  6 LEU N   B - A  6 LEU CB  B mod.= 2.446 id.= 1.530 dev= -0.916 
 sig.= 0.020
 A  6 LEU CB  A - A  6 LEU HB2 A mod.= 0.969 id.= 1.521 dev=  0.552 
 sig.= 0.020
 A

 Rfree goes form 17 to 28 and R from 15 to 25.
 Coot map looks like a bunch of busted insect parts.


 I use the exact same input using ccp4 6.1.13 and Refmac 5.5 and all is good. 
 I am forced to use the
 old ccp4 and refmac to publish. Rf 17 R 15.
 thanks

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

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

[LEGRAND Pierre]

Dear Ed,
Not in my case. I still do *restrained* refinement.
I use:
refi type REST -
resi MLKF -
meth CGMAT -
bref MIXED
ncyc 10
blim 0.1 200.0

With both: weight MATRIX 50 or weight AUTO it gives the same problem.
I have also tested the latest refmac5 version (Refmac_5.6.0119) and latest 
dictionaries (refmac_dictionary_v5.31), but it still produce the same error, 
directly from the first cycle.

I can give more details and files off-list if requested.
Cheers,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Ed Pozharski 
[epozh...@umaryland.edu]
Date d'envoi : vendredi 28 octobre 2011 16:00
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

Just to verify, is this by any chance *unrestrained* refinement?

On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Kenneth A. Satyshur,

 what is your weight set to? If it is set to 'auto', try setting it to a
 specific value and lower that value until the explosion stops.

 If this happens at low matrix values (at 1.24A it should be way above 5
 or 10 for a well refined structure), your resolution might not be 1.24A,
 i.e., you may have integrated noise (check I/sigI over resolution shells).

 Tim

 P.S.: I wonder what power somebody might have to _force_ you use a
 specific software version...


 On 10/28/2011 03:48 AM, Kenneth A. Satyshur wrote:
  Has anyone had problems with Refmac 5.6? I tried refining our stucture at 
  1.24 A,
  aniso with H in riding position and it just exploded! I get error in 
  distances such as
 
  Standard  External   All
  Bonds:  3270 0  3270
 Angles:  4923 0  4923
Chirals:   214 0   214
 Planes:   368 0   368
   Torsions:   957 0   957
  ---
 
   Number of reflections in file  90428
   Number of reflections read  90428
 
 
   CGMAT cycle number =  1
 
   Bond distance outliers 
  
 
  Bond distance deviations from the ideal 10.000Sigma will be monitored
 
  A  5 PRO C   A - A  5 PRO HB1 A mod.= 3.344 id.= 1.329 dev= -2.015 
  sig.= 0.014
  A  5 PRO C   B - A  5 PRO HB1 B mod.= 2.997 id.= 1.329 dev= -1.668 
  sig.= 0.014
  A  5 PRO HB1 A - A  5 PRO HG1 A mod.= 2.292 id.= 1.458 dev= -0.834 
  sig.= 0.021
  A  5 PRO HB1 A - A  6 LEU HD23A mod.= 7.407 id.= 0.860 dev= -6.547 
  sig.= 0.020
  A  5 PRO HB1 B - A  5 PRO HG1 B mod.= 2.247 id.= 1.458 dev= -0.789 
  sig.= 0.021
  A  5 PRO HB1 B - A  6 LEU HD23B mod.= 6.529 id.= 0.860 dev= -5.669 
  sig.= 0.020
  A  5 PRO HG1 A - A  5 PRO HD1 A mod.= 2.267 id.= 0.980 dev= -1.287 
  sig.= 0.020
  A  5 PRO HG1 A - A  6 LEU N   A mod.= 4.860 id.= 1.530 dev= -3.330 
  sig.= 0.020
  A  5 PRO HG1 A - A  6 LEU HD21A mod.= 6.129 id.= 1.525 dev= -4.604 
  sig.= 0.021
  A  5 PRO HG1 B - A  5 PRO HD1 B mod.= 2.236 id.= 0.980 dev= -1.256 
  sig.= 0.020
  A  5 PRO HG1 B - A  6 LEU N   B mod.= 4.922 id.= 1.530 dev= -3.392 
  sig.= 0.020
  A  5 PRO HG1 B - A  6 LEU HD21B mod.= 6.664 id.= 1.525 dev= -5.139 
  sig.= 0.021
  A  6 LEU N   A - A  6 LEU CA  A mod.= 1.467 id.= 0.970 dev= -0.497 
  sig.= 0.020
  A  6 LEU N   A - A  6 LEU HA  A mod.= 2.005 id.= 0.970 dev= -1.035 
  sig.= 0.020
  A  6 LEU N   A - A  6 LEU CB  A mod.= 2.497 id.= 1.530 dev= -0.967 
  sig.= 0.020
  A  6 LEU N   B - A  6 LEU CA  B mod.= 1.469 id.= 0.970 dev= -0.499 
  sig.= 0.020
  A  6 LEU N   B - A  6 LEU HA  B mod.= 2.032 id.= 0.970 dev= -1.062 
  sig.= 0.020
  A  6 LEU N   B - A  6 LEU CB  B mod.= 2.446 id.= 1.530 dev= -0.916 
  sig.= 0.020
  A  6 LEU CB  A - A  6 LEU HB2 A mod.= 0.969 id.= 1.521 dev=  0.552 
  sig.= 0.020
  A
 
  Rfree goes form 17 to 28 and R from 15 to 25.
  Coot map looks like a bunch of busted insect parts.
 
 
  I use the exact same input using ccp4 6.1.13 and Refmac 5.5 and all is 
  good. I am forced to use the
  old ccp4 and refmac to publish. Rf 17 R 15.
  thanks
 
  --
  Kenneth A. Satyshur, M.S.,Ph.D.
  Associate Scientist
  University of Wisconsin
  Madison, Wisconsin 53706
  608-215-5207

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

 GPG Key ID = A46BEE1A

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[ccp4bb] RE : [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

[LEGRAND Pierre]

Thanks all for your suggestions,

Here's a little summary of my recent tests.
I am currently using WEIGHT AUTO and BREF MIXED with a pdb file that contains 
ANISOU definition for all atoms except hydrogens.

Final results for BREF MIXED refinement :

  InitialFinal
   R factor0.0880   0.0867
 R free0.0932   0.0925
 Rms BondLength0.0174   0.0189
  Rms BondAngle2.8613   2.8740
 Rms ChirVolume0.1076   0.1146

Final results for BREF ANISO refinement:

  InitialFinal
   R factor0.0880   0.0874
 R free0.0932   0.0956
 Rms BondLength0.0174   0.0189
  Rms BondAngle2.8613   2.8683
 Rms ChirVolume0.1076   0.1151

In the WEIGHT AUTO run refmac5 uses:  Weight matrix137.7641
Final results for WEIGHT MATRIX 60 refinement:

  InitialFinal
   R factor0.0880   0.0872
 R free0.0932   0.0922
 Rms BondLength0.0174   0.0181
  Rms BondAngle2.8613   2.8632
 Rms ChirVolume0.1076   0.1134

I have just sent Garib different data files so that he can reproduce the 
problem one can have with H naming/dictionaries definitions.
When it happens, from the same initial pdb with WEIGHT AUTO and BREF MIXED 
but a differente cif definition (from the latest refmac_dictionary_v5.31) here 
what it gives:

  InitialFinal
   R factor0.0880   0.1820
 R free0.0932   0.1869
 Rms BondLength2.8573   2.3884
  Rms BondAngle   35.7010  34.7547
 Rms ChirVolume   10.5335   4.2429

I hope it helps to clarify the situation,
Cheers,
Pierre


De : Garib Murshudov [garib.murshu...@gmail.com] de la part de Garib N 
Murshudov [ga...@mrc-lmb.cam.ac.uk]
Date d'envoi : vendredi 28 octobre 2011 17:49
À : LEGRAND Pierre
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Dear Pierre

Resolution seems to be good enough for full anisotropic refinement. Why don't 
you try this and see if it stabilises refinement.

regards
Garib

On 28 Oct 2011, at 16:22, LEGRAND Pierre wrote:

Dear Ed,
Not in my case. I still do *restrained* refinement.
I use:
refi type REST -
   resi MLKF -
   meth CGMAT -
   bref MIXED
ncyc 10
blim 0.1 200.0

With both: weight MATRIX 50 or weight AUTO it gives the same problem.
I have also tested the latest refmac5 version (Refmac_5.6.0119) and latest 
dictionaries (refmac_dictionary_v5.31), but it still produce the same error, 
directly from the first cycle.

I can give more details and files off-list if requested.
Cheers,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Ed Pozharski 
[epozh...@umaryland.edu]
Date d'envoi : vendredi 28 octobre 2011 16:00
À : CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

Just to verify, is this by any chance *unrestrained* refinement?

On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Kenneth A. Satyshur,

what is your weight set to? If it is set to 'auto', try setting it to a
specific value and lower that value until the explosion stops.

If this happens at low matrix values (at 1.24A it should be way above 5
or 10 for a well refined structure), your resolution might not be 1.24A,
i.e., you may have integrated noise (check I/sigI over resolution shells).

Tim

P.S.: I wonder what power somebody might have to _force_ you use a
specific software version...


On 10/28/2011 03:48 AM, Kenneth A. Satyshur wrote:
Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24 
A,
aniso with H in riding position and it just exploded! I get error in distances 
such as

   Standard  External   All
   Bonds:  3270 0  3270
  Angles:  4923 0  4923
 Chirals:   214 0   214
  Planes:   368 0   368
Torsions:   957 0   957
---

Number of reflections in file  90428
Number of reflections read  90428


CGMAT cycle number =  1

    Bond distance outliers 


Bond distance deviations from the ideal 10.000Sigma will be monitored

A  5 PRO C   A - A  5 PRO HB1 A mod.= 3.344 id.= 1.329 dev= -2.015 
sig.= 0.014
A  5 PRO C   B - A  5 PRO HB1 B mod.= 2.997 id.= 1.329 dev= -1.668 
sig.= 0.014
A  5 PRO HB1 A - A  5 PRO HG1 A mod.= 2.292 id.= 1.458 dev= -0.834 
sig.= 0.021
A  5 PRO HB1 A - A  6 LEU HD23A mod.= 7.407 id.= 0.860 dev= -6.547 
sig.= 0.020
A  5 PRO HB1 B - A  5 PRO HG1 B mod.= 2.247 id.= 1.458 dev= -0.789 
sig.= 0.021
A  5 PRO HB1 B - A  6 LEU HD23B mod.= 6.529 id.= 0.860 dev= -5.669

Re: [ccp4bb] Problem with NCS detection in Parrot

[LEGRAND Pierre]

Hi Florian,

I have found that, in some cases, playing with -ncs-mask-filter-radius can help 
parrot to successfully detect and apply ncs averaging.
In one recent case, with 8 molecules where NCS was not found without this 
option, values from 14 to 30 angstroms worked (but gave maps of variable 
quality).
I don't know what's the default value for this.

Best regards,

Pierre Legrand, PROXIMA-1
Phone-office   +33 1 69 35 96 60
Phone-beamline +33 1 69 35 97 38
http://www.synchrotron-soleil.fr/Recherche/LignesLumiere/PROXIMA1

-Original Message-
From: CCP4 bulletin board on behalf of Florian Schmitzberger
Sent: Fri 9/3/2010 9:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with NCS detection in Parrot
 
Dear All,

I am encountering a problem when using Parrot (for combined density  
modification and non crystallographic symmetry (NCS) averaging) in  
ccp4 6.1.13, run via ccp4i.

Parrot does not detect the (2-fold) NCS present among my heavy atom  
substructure with 20 seleniums (the pdb was output by Phaser-EP,  
single chain ID, and is read by Parrot from what I can tell). I have  
tried a to split the NCS related heavy atoms into separate chains, but  
Parrot does still not appear to detect any NCS (error message:  
WARNING: No NCS found from heavy atoms).

The Professs program seems to detect the NCS readily. Unfortunately, I  
don't think it is possible to input externally determined NCS  
operators into Parrot.

Regards,

Florian

---
Florian Schmitzberger
Biological Chemistry and Molecular Pharmacology
Harvard Medical School
250 Longwood Avenue, SGM 130
Boston, MA 02115, US
Tel: 001 617 432 5602

[ccp4bb] Post-doctoral Position in biochemistry/structural biology at PROXIMA-1/SOLEIL.

[LEGRAND Pierre]

Dear members,

We are seeking a motivated young scientist with a background in structural 
biology and an interest in
instrumentation and/or methodology. As a member of the PROXIMA 1 beamline team, 
your main scientific mission
will be to contribute to a research program focused on the structural 
characterization of proteins and complexes
involved in RNA degradation in trypanosomatid parasites. You will also be 
involved in user support activities.

The position will open in November 2010.
For further information, contact: beatriz.guimar...@synchrotron-soleil.fr

Qualifications  Experience:
The candidate holds a Ph.D. or equivalent in science related to structural 
biology.
You must have expertise in one or several of the following domains: production, 
purification and crystallization of
recombinant proteins, X-ray crystallography, structure determination and 
analysis. Knowledge of biophysical
characterization methods such as small angle X-ray scattering, circular 
dichroism, calorimetry, FTIR, Raman, will be
much appreciated.

General conditions:
The offer concerns a Post-doctoral contract for a two year-period. The place of 
work will be at Synchrotron SOLEIL,
which is located in the Paris suburbs (Saint-Aubin).
Applications should include a motivation letter and Curriculum Vitae with the 
addresses of two referees.
Applications should be preferably registered directly on the:
http://candidature.synchrotron-soleil.fr/VotreCandidature/ with the reference: 
Post-Doc PROXIMA 1.
Deadline for submission of applications is 10th September 2010.

http://www.synchrotron-soleil.fr/images/File/soleil/DivisionAdministration/Personnel/SOLEIL_postDoc_PROXIMA%201.pdf

Best regards
Beatriz Guimaraes

[ccp4bb] RE : [ccp4bb] Rotation search using the Patterson in a non-spherical neighbourhood of the origin

[LEGRAND Pierre]

Hi,

I think there is something like that described in this paper:
F. M. D. Vellieux An enveloped cross rotation function
J. Appl. Cryst. (1995). 28, 834-836
If I remember correctly, the calculations where done using x-plor scripts.

Pierre
Proxima-1 Team
Synchrotron-SOLEIL

 Message d'origine
De: CCP4 bulletin board de la part de Pietro Roversi
Date: mer. 28/11/2007 18:04
À: CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Rotation search using the Patterson in a non-spherical 
neighbourhood of the origin
 
Dear everyone,
   is any of the currently available
molecular replacement programs capable of accepting a
description of an ellipsoid (rather than the radius of a sphere)
to define the portion of the Patterson around the origin to be
used in a Molecular
Replacement rotation search? Our search model is an elongated
object and we are searching in a cell with a=205 b=100 c=21
Angstrom ... ;-)

Ciao

Pietro
-- 
Pietro Roversi
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3ER, England UK
Tel. 0044-1865-275385