Re: [ccp4bb] CH-bond length discrepancies

[Santarsiero, Bernard D.]

It totally depends on what you define as your C-H bond length.

For XRD work, the C-H is the distance between the electron
center-of-masses. For  neutron or high-resolution XRD work, you can
determine the distance between the nuclear center-of-masses.  They are
different by about 0.1A.  The electron COM for hydrogen is substantially
shifted along the bond towards the carbon atom.

I did a very precise determination of 1,1-dicyclobutanedicarboxylic acid
at 20K, and the C-H bond lengths averaged to 0.991A, and far shorter than
the 1.096A you'd expect from a neutron diffraction study.

The VDW distances shouldn't be that important since the potential isn't
that sensitive with a difference of 0.1A.  If you have to restrain C-H
distances for XRD refinement, then they should be shortened.

BDS



On Sat, April 29, 2017 8:22 am, benjamin bax wrote:
>
>
>
> 'Most distances   between bonded  atoms   weresettled longago 
> to  highaccuracy,   but,in  the caseof  
> hydrogens,  the values  in  common  use often   differ  by
>   as  muchas  20%.'
>
> Phenix/   MolProbity  HydrogenParameter   Update
>
> Deis, L. N., Verma, V., Videau, L. L., Prisant, M. G., Moriarty, N. W.,
>
> Headd, J. J., Chen, V. B., Adams, P. D., Snoeyink, J., Richardson, J. S. &
> Richardson, D. C. (2013). Comput. Crystallogr. Newsl. 4, 9–10.
>
>
>
> On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:
>
> Dear Fellows of the Bond,
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma deviations in the carbon-hydrogen bond distances.
> Out of curiosity, I then used refmac to calculate riding Hs for the same
> model, and at least in one instance (N-H backbone) there are
> significant differences between Molprobity and Refmac H bond distances
> (differences to the QM distances in other
> instances I find interesting, but less relevant for us).
>
> The riding H vs Molprobity presumably should be consistent, because if we
> use them in VDW restraints but
> they differ from the validation target, systematic bias will occur. I have
> no feel how significant that effect
> might be – maybe someone more erudite can comment.
>
> Examples
>
> distance  MP   REF QM
> backbone N-H   0.861.011.00
> phenyl C-H 0.930.931.09
>
> Best, BR
>
> PS: If someone has accurate experimental values for CH distances I’d
> appreciate a link.
> No access to CSD.
>
> --
> 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
> --
>
>
> Dr Ben Bax
>
> York Structural Biology Laboratory,
> Department of Chemistry,
> University of York,
> York YO10 5DD
>
> ben.d.v@gmail.com
>
>
>
>
>
>


-- 
Bernard D. Santarsiero
Associate Director, UI Health Systems Biorepository
Research Professor
Center for Biomolecular Sciences and the
  Department of Medicinal Chemistry and Pharmacognosy
Center for Structural Biology
Center for Clinical and Translational Science
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds
http://scholar.google.com/citations?user=fGauLBMJ

[ccp4bb] REFMAC - TWIN OPTION

[Santarsiero, Bernard D.]

Can someone point me to bulletpoint documentation on using the twin
refinement in CCP4?

Here's what I did.

1.  I'm in space group P3, and the see a very clean diffraction pattern
that looks like one single lattice. Very clean spots, so merohedral
twinning.

2.  You can use various programs to estimate the twin fraction and select
various twin laws.

3.  You run DETWIN in the UTILITIES section of DATA REDUCTION and
ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected
amplitudes. The FMEAN changes to something like FMEAN_detw. You have to
select a twin fraction, but does it matter what the twin factor you assign
is?  (It seems to get refined, or just estimated, in refinement?)

4.  There are potentially 3 twin laws, so do you run DETWIN three times? 
You can, in fact, get amplitudes that are FMEAN_detw_detw_detw.  I've run
it once and three times, and seems to give the same result in REFMAC
refinement.

5.  Select the Free R subset. Will uniqueify choose correctly?

6.  In REFMAC, it looks for the F_detw amplitude, or you can select it.
Then it seems to select and test three twin laws, even if you only ran
DETWIN once, with one selected twin law. It tests if the twin laws give
low R(merge).  If not, it tosses them out. It seems like the R(merge)
calculation depends on the starting model, and not just on the modified
Fobs data. It also seems like it tries to calculate the twin fraction, and
then refine the structure. Or, is it just giving an estimate, and I need
to go back to original data and rerun DETWIN?

7.  I tried to work with intensities instead of amplitudes, and it can
blow up. I've also refined, got a good refinement (3 twin laws, each with
twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of
the structure, and it blows up, suggesting no twinning, but Rs around 35%.

Does REFMAC refine the twin fraction?
Do I have to assign a twin fraction in DETWIN, or does it just set up the
relationships between reflections and amplitudes?
Should I try to work with intensities or amplitudes.  The calculation is
presumably done on intensities, but seems to be more unstable using that
option.

I haven't tried the PHENIX option. Just a quick step-by-step guide on what
to do would be useful.

Thanks,

Bernie
-- 
Bernard D. Santarsiero
Research Professor
Center for Structural Biology
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds
http://scholar.google.com/citations?user=fGauLBMJ

[ccp4bb] ATP library file in REFMAC - Part II

[Santarsiero, Bernard D.]

I appreciate all of the comments and suggestions on how to locate a better
CIF file for ATP. I adopted the suggestion of Boaz, and generated a new
ATP.cif file, and refined one of my structures.

The validation server still uses substantially different target bond
lengths and angles, so there is better agreement, but I still get flags.
Both bond length and angles target values are more realistic than what was
used in the REFMAC ATP.cif file, but I still find fault with the target
values.

For example, the bond lengths and angles around PB, the beta P atom, range
from 104.4-108.7deg in the "grade" file, and are unrealistic since they
are all less than the tetrahedral angle. The CIF also targets one P-O as a
single and the other as formally a double bond, but most crystallographic
studies indicate at least some delocalization over both internal oxygen
atoms, and a slight compression of that angle.  The validation server has
an "ideal" target value of 101.66deg which is surely contracted from a
more reasonable value near 105deg.

One approach that would be useful is to consider refinement on special
groups, like phosphate, with structural parameters, instead of actual
target bond lengths and angles, so R1 for the two PB-O1B and PB-O2B
distances, and R2 for the two PB-O3A and PB-O3B distances, and pairs of
angle restraints incorporating a complete delocalization model. See, for
example, Murray-Rust, Burgi, and Dunitz, J. Am. Chem. Soc., 97, 921
(1975), or Tamasi at al., The Open Crystallography Journal, 3, 1 (2010).
This could be used to directly address questions about delocalization and
hydrolytic capacity, rather than trying to determine then from bond
lengths.

Bernie




On Wed, August 27, 2014 2:05 pm, Boaz Shaanan wrote:
>   Or use Grade:
> http://grade.globalphasing.org/cgi-bin/grade/server.cgi
>   which gives the correct bond length.
>   Boaz
>
>   Boaz Shaanan, Ph.D.
>  Dept. of Life Sciences
>  Ben-Gurion University of the Negev
>  Beer-Sheva 84105
>  Israel
>
>  E-mail: bshaa...@bgu.ac.il
>  Phone: 972-8-647-2220  Skype: boaz.shaanan
>  Fax:   972-8-647-2992 or 972-8-646-1710
>
>   From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> Bernard D Santarsiero [b...@uic.edu]
>  Sent: Wednesday, August 27, 2014 6:12 PM
>  To: CCP4BB@JISCMAIL.AC.UK
>  Subject: [ccp4bb] ATP library file in REFMAC
>
> I recently refined a structure in CCP4/REFMAC with ATP in the
> structure. Upon submission to Acta for publication, the wwPDB
> validation report was run. Several things were flagged, including the
> C4-C5 bond in the adenosine moiety as being too long. It generally
> refines to 1.46-1.47A. The "ideal" distance in the
> validation report is 1.38A, and the upon review of the ATP.cif file in
> the REFMAC library, the target distance is 1.49A (and listed as a
> double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up
> gives the target bond length as 1.404A.
>   Where can I grab a revised ATP.cif file? I guess I'll need to re-refine
> all of my structures and re-run the validation report.BTW, I also
> looked at the PDB_REDO structure report for my structure, and can't
> reproduce the Rcryst and Rfree values with the same model.
>   Bernie --

Re: [ccp4bb] 18A rule reference

[Santarsiero, Bernard D.]

Divide by 11 if you count all atoms, including H-atoms; divide by 20-22 if
you only count non-H-atoms, to get the approximately number of atoms in
the unit cell.


On Mon, May 5, 2014 6:07 am, Natalie Tatum wrote:
> Hi all,
>
> I've had an interesting question from an undergradute student, asking if
> there's any specific reference for the "18Å rule of thumb" in small
> molecule crystallography for dividing the volume of a unit cell by 18 for
> the approximate number of non-hydrogen atoms.
>
> I'm afraid my google-fu has failed me, but I was curious as to whether
> there is a reference associated with the practice of if it's just one of
> those handy little pieces of advice for crystal screening.
>
> Thanks,
>
> Natalie

Re: [ccp4bb] Td ions in refmac

[Santarsiero, Bernard D.]

Is there a reason why you must use restraints with metal coordination?

The main reasons that you use restraints in protein refinement is to
reduce the number of free variables in the refinement, and because the
"resolution" isn't sufficient to resolve two atoms separated by the
typical carbon-carbon distance of 1.5A.

In a metal complex, the distances are roughly 2A or greater, and the metal
position is well-determined since it has a large number of electrons.  I
would just restrain the protein part of the structure, and let the metal
refine freely.

Bernie Santarsiero


On Fri, June 7, 2013 9:25 am, Roger Rowlett wrote:
> Well, when I solved a structure for a protein-rhenium adduct I had to
> manually code a restraint file for the rhenium tricarbonyl fragment,
> which is octahedral overall (with proteins ligands and waters), and had
> several different types of bond distances for the various ligands. I
> started with an incorrect description of a similar ligand cif file from
> HIC-UP and hand-edited the cif file to suit. It seems to me it should be
> possible (although somewhat painful) to write a similar restraint file
> (geometry + bond lengths) for ZN.
>
> Cheers,
>
> ___
> Roger S. Rowlett
> Gordon & Dorothy Kline Professor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: rrowl...@colgate.edu
>
> On 6/7/2013 9:23 AM, Tim Gruene wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> Hi Jim,
>>
>> the chemical basis would be that the Zn connects to all four S atoms,
>> and if they are indistinguishable, all Zn-S distances should be alike.
>>
>> But the S-atoms are not bonded to each other, hence they want to have as
>> much distance from each other as possible. Since they are four, this
>> makes them a tetrahedron.
>>
>> I am not aware of a more automated/ simpler way of turning the angles
>> at the metal into restraints other than calculating the S-S distances
>> with a pocket calculator, although that does not mean they do not exist.
>>
>> Cheers,
>> Tim
>>
>> On 06/07/2013 11:56 AM, James Naismith wrote:
>>> Andrew Leslie made a similar suggestion for using CB to S
>>> distances.
>>>
>>> Both make me unhappy for the reason that there is not a clear
>>> chemical basis to them (Tim's has more a chemical basis) and how
>>> would I choose the distance. (I can measure it from a known
>>> structure)
>>>
>>>
>>> I have previously experimented with Tim's (works). I am searching
>>> for anyone who knew a simple way to restrain metal ion geometry in
>>> remfac based on angles at metal.
>>>
>>> best Jim
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 7 Jun 2013, at 10:14, Tim Gruene 
>>> wrote:
>>>
>>> Dear James,
>>>
>>> I am not sure I fully picture what your coordination looks like,
>>> but my guess is that if you include distance restraints between the
>>> S-atoms you can distinguish between a tetrahedral geometry and a
>>> square pyramid.
>>>
>>> You could use external restraints in refmac - just make a dummy
>>> run with prosmat to get the syntax right and copy and modify a few
>>> lines tailored to your problem.
>>>
>>> Best, Tim
>>>
>>> On 06/07/2013 10:39 AM, James Naismith wrote:
>> Thanks for this other suggestions similar (see  below.) My
>> problem is not the distances per se, these restrain fine to
>> 2.3A
>>
>> I am relatively low resolution and my problem is with just
>> distance restraints I move to a square planar arrangement. I
>> suspect this is a feature of the geometry restraints
>> dominating refinement (c'est la vie at low res). I do not
>> force Zn to be anything (the cif file just has a distance) I
>> think.
>>
>> What I need to do is create another restraint someone how
>> that imposes a Td geometry.
>>
>> What I cannot figure how to do is set this up because it
>> involves 5 residues (4 cys and 1 Zn).
>>
>> best Jim
>>
>> Jim Naismith BSRC, North Haugh j...@st-andrews.ac.uk
>>
>> Google scholar is free and tracks your outputs, mine are
>> http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMJ
>>
>>
>>
>> ResearcherID H-3408-2012; SCOPUS_ID 7005691850
>> http://www.researchgate.net/profile/James_Naismith/
>>
>> The University of St Andrews is a charity registered in
>> Scotland : No SC013532k
>>
>>
>>
>>
>> On 6 Jun 2013, at 16:11, Roger Rowlett
>>  wrote:
>>
>>> You can find instructions for restraining Zn-ligand
>>> distances here:
>>>
>>> http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement&highlight=metal%20ion#Restraining_metal_ligand_distances_during_refinement_in_REFMAC
>>>
>>>
>>>
>>>
>>>
>>>
>> Using this method, only Zn-ligand bond distances are restrained.
>>> REFMAC can usually find on its own certain Zn-atom linkage

[ccp4bb] Phaser - changing number of clashes parameter

[Santarsiero, Bernard D.]

The new CCP4I interface for PHASER removed the menu item where you could
change the number of clashes. It's not set as a default to 5% of the
number of C-alpha atoms. Where is the default file?

I found the phaser_MR.def file in share/ccp4i/tasks, and changed the
parameter value, but it still used the default of 5%.

Thanks,

Bernie
-- 
Bernard D. Santarsiero
Research Professor
Center for Pharmaceutical Biotechnology and the
 Department of Medicinal Chemistry and Pharmacognosy
Center for Structural Biology
Center for Clinical and Translational Science
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

[Santarsiero, Bernard D.]

No, I listed a few recent ones


V. Gaur, et al., Plant Physiol., 152(4), 1842-1850 (2010)

O. Antipova, J Biol Chem. 2010 Mar 5;285(10):7087-96. Epub 2010 Jan 6.

Y. Nakajima, J Bacteriol. 2008 Dec;190(23):7819-29. Epub 2008 Sep 26.

S. Stayrook, Nature. 2008 Apr 24;452(7190):1022-5.

Many MIRAS, so the MIR part helped to get forms, and then collected with AS.



On Wed, June 6, 2012 3:42 pm, Boaz Shaanan wrote:
> So if get the gist of the thread right, am I correct in assuming that the
> last protein structures to be solved strictly by MIR  are
> haemoglobin/myoglobin, lysozyme and chymotrypsin and perhaps one or two
> more in the late sixties? In which case the answer  to the original
> question about MIR being obsolete, is "yes it is since a long time"?
>
>   Boaz
>

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

[Santarsiero, Bernard D.]

Remember that it's all relative to the length of the FP vector. If your FP
vector is small, then the f" component can substantially change the phase,
even with a small f" component. So if you have measured a number of
relatively weak reflections with minimal error, there is a substantial
anomalous signal.  If you have a huge FP vector, then you won't see much
of a phase change.  Bernie


On Wed, June 6, 2012 10:02 am, Dyda wrote:
>>I suspect that pure MIR (without anomalous) was always a fiction. I doubt
>> that anyone has ever used it. Heavy atoms always give
>>an anomalous signal
>
>>Phil
>

Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line

[Santarsiero, Bernard D.]

Most beamlines have attenuators, so there's little reason to collect
multiple sweeps. We always collect 360deg. Since it's a small molecule,
and usually fairly large and robust, you can warm it up, nudge it in a
different direction with a pin (we use sterile, disposable acupunture
needle), and refreeze it in the cryostream. Then do a second sweep in a
different orientation.

I recommend moving the beam energy to 15.5KeV or higher to compress the
diffraction image. Collect with 5-10deg widths. We can typically get the
detector to around 70-80mm. You need to get to 0.85A resolution or better
for good, stable refinement, and Acta Cryst. requires that resolution for
publication.  Often you need the low-resolution data and data to better
than 1A to help with the sigma2 relationships in direct methods.

You see both primary and secondary extinction, and that extinction can be
anisotropic, so the SWAT option in SHELX is most useful. Otherwise, the
overall scale factor is off, typically overestimated by the strong
low-resolution reflection intensities, with the result that the
anisotropic Gaussian displacement parameters may become non-positive
definate.

Bernie

On Wed, February 8, 2012 12:46 pm, Jens Kaiser wrote:
> Giorgo,
>   We have done that routinely for quite some time now. We had problems
> when using a normal CCD detector, where we had to collect two or three
> sweeps to avoid overloads (see below). Since we have the PILATUS this is
> not necessary anymore and the data behaves fine. "Problems" still
> persisting are: we have only a single axis goniometer, which can lead to
> low completeness in P1 and P-1. Highest energy (17keV) and closest
> distance (188mm) at our beamline have many SM crystals (even the ones
> that "don't diffract" in house -- that is a 300 or 500 u sealed tube)
> with an I/sig of 5-10 at the edge of the detector. Crunch, Acorn,
> ShelxCDE and ShelxS don't have any problem with any of the data we
> collected to <0.9A resolution. The multipass caused some inexplicable
> non definite positives during refinement. We haven't tracked that down
> systematically, so it might just have happened haphazardly.
>
> HTH,
>
> Jens
>
> On Wed, 2012-02-08 at 11:41 +, Giorgio Giardina wrote:
>> Hello,
>> I have some interesting small molecule xtals.
>> I was wondering if it is possible to collect a small molecule data-set
>> using a sincrotron macromolecular  xtallography beam line, maybe with a
>> very low beam intensity and moving the detector as close as possible?
>> Has anybody experienced that?
>> And if I get the images back home,  can I process them using standard
>> macromolecular software or do I need ab-initio special programs?
>> Will MR work for phasing?
>>
>> Thanks in advance,
>> Giorgio
>
>


-- 
Bernard D. Santarsiero
Research Professor
Center for Pharmaceutical Biotechnology and the
 Department of Medicinal Chemistry and Pharmacognosy
Center for Structural Biology
Center for Clinical and Translational Science
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds

[ccp4bb] Coot, RH6.1 x86 linux

[Santarsiero, Bernard D.]

I just installed CCP4-6.2.0 and COOT on a Red Hat v6.1, x86, linux
workstation. Some of the menus, along the right edge, are gray buttons on
gray background. Where is the preferences file to change the colors of the
menu buttons? The menus across the top of the window are fine.

Also, idiffdisp is unable to view a file. It loads the idiffdisp window,
but gives error messages. Is there a log file that I can scan? I think I'm
missing some library files for x86.

Bernie

-- 
Bernard D. Santarsiero
Research Professor
Center for Pharmaceutical Biotechnology and the
 Department of Medicinal Chemistry and Pharmacognosy
Center for Structural Biology
Center for Clinical and Translational Science
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds

Re: [ccp4bb] Newbie Installation Question

[Santarsiero, Bernard D.]

I've had problems too. Some of the files are non-readable, so you need to
do a

sudo chmod -R a+r *

to make them readable. Also it looks like the libraries changed a bit (at
least for ADP).

Bernie

On Fri, July 29, 2011 2:08 pm, Yuri wrote:
> Dear all,
> I have just downloaded and installed the ccp4-6.2.0.
> It says all I should do next is source the /setup-scripts/csh/ccp4.setup
> file... I have done that, but I cannot launch the program...
> Any help is welcome...(it is probably something really stupid on my
> part...)
> Best,
>

Re: [ccp4bb] small lysozyme crystals?

[Santarsiero, Bernard D.]

That's a really old paper. You can purchase the lysozyme from Hampton
Research and it's fine. The recipe is available from the Hampton Research
page:

http://hamptonresearch.com/product_detail.aspx?cid=28&sid=173&pid=524

Grow them a low temp and you can stop them when they are the right size. 
I favor that over room temp. They grow fast and large, but don't give a
good R(merge) as when grown at a lower concentration and slower.

Bernie



On Tue, July 26, 2011 5:09 pm, mjvdwo...@netscape.net wrote:
>
>
>  James,
>
> I would have a look at the paper by Judge et al:
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300446/pdf/10465769.pdf
>
>
> Specifically, in this paper you will find that the crystallization
> behavior of lysozyme changes drastically with pH. At the time the paper
> wasn't really written to manipulate for small crystal size, but looking
> back at the paper (specifically Fig 5), it appears that you can read the
> conditions that will give you crystals around the size you want.
>
> Not re-reading the paper, quoting from memory (which we all think is
> better than it really is), it is important to use good quality lysozyme to
> get reproducible results. Good quality probably means freshly purified
> from fresh (farm-acquired) eggs. I am not kidding you, it makes a big
> difference. Also, I am going out on a limb to say (I know you know this)
> that the buffer preparation method matters a lot. Taking sodium acetate
> solution and pH-ing it with HCl will give very different results from
> taking acetic acid and pH-ing it with NaOH (because the ionic strength of
> the buffer is not the same). Lysozyme crystallizes so easily that we tend
> to forget tedious details.
>
> Hope this helps. This paper will probably give you some ideas in the right
> direction.
>
> Mark van der Woerd
>
>
>
>
>
>

Re: [ccp4bb] problem of conventions

[Santarsiero, Bernard D.]

Dear Ian,

Well, "it" *IS* broke. If you are running some type of process, as you
implied in referring to LIMS, then there is a step in which you move from
the crystal system and point group to the actual space group. So, at that
point you identify P22121. The next clear step, automatically by software,
is to convert to P21212, and move on. That doesn't take an enormous amount
of code writing, and you have a clear trail on how you got there.

To be even more intrusive, what if you had cell parameters of 51.100,
51.101, and 51.102, and it's orthorhombic, P21212. For other co-crystals,
soaks, mutants, etc., you might have both experimental errors and real
differences in the unit cell, so you're telling me that you would process
according to the a < b < c rule in P222 to average and scale, and then it
might turn out to be P22121, P21221, or P21212 later on? When you wish to
compare coordinates, then you have re-assign one coordinate data to match
the other by using superposition, rather than taking on an earlier step of
just using the conventional space group of P21212?

Again, while I see use of the a < b < c rule when there isn't an
overriding reason to assign it otherwise, as in P222 or P212121, there
*is* a reason to stick to the convention of one standard setting. That's
the rationale on using P21/n sometimes vs. P21/c, or I2 vs C2, to avoid a
large beta angle, and adopt a non-standard setting.

Finally, if you think it's fine to use P22121, then can I assume that you
also allow the use of space group A2 and B2?

Bernie


Bernie







On Fri, April 1, 2011 8:46 am, Ian Tickle wrote:
> Dear Gerard,
>
> The theory's fine as long as the space group can be unambiguously
> determined from the diffraction pattern.  However practice is
> frequently just like the ugly fact that destroys the beautiful theory,
> which means that a decision on the choice of unit cell may have to be
> made on the basis of incomplete or imperfect information (i.e.
> mis-identification of the systematic absences).  The 'conservative'
> choice (particularly if it's not necessary to make a choice at that
> time!) is to choose the space group without screw axes (i.e. P222 for
> orthorhombic).  Then if it turns out later that you were wrong it's
> easy to throw away the systematic absences and change the space group
> symbol.  If you make any other choice and it turns out you were wrong
> you might find it hard sometime later to recover the reflections you
> threw away!  This of course implies that the unit-cell choice
> automatically conforms to the IT convention; this convention is of
> course completely arbitrary but you have to make a choice and that one
> is as good as any.
>
> So at that point lets say this is the 1970s and you know it might be
> several years before your graduate student is able to collect the
> high-res data and do the model-building and refinement, so you publish
> the unit cell and tentative space group, and everyone starts making
> use of your data.  Some years later the structure solution and
> refinement is completed and the space group can now be assigned
> unambiguously.  The question is do you then revise your previous
> choice of unit cell risking the possibility of confusing everyone
> including yourself, just in order that the space-group setting
> complies with a completely arbitrary 'standard' (and the unit cell
> non-conventional), and requiring a re-index of your data (and
> permutation of the co-ordinate datasets).  Or do you stick with the IT
> unit cell convention and leave it as it is?  For me the choice is easy
> ('if it ain't broke then don't fix it!').
>
> Cheers
>
> -- Ian
>
> On Fri, Apr 1, 2011 at 1:40 PM, Gerard Bricogne 
> wrote:
>> Dear Boaz,
>>
>>     I think you are the one who is finally asking the essential
>> question.
>>
>>     The classification we all know about, which goes back to the 19th
>> century, is not into 230 space groups, but 230 space-group *types*, i.e.
>> classes where every form of equivalencing (esp. by choice of setting)
>> has
>> been applied to the enumeration of the classes and the choice of a
>> unique
>> representative for each of them. This process of maximum reduction
>> leaves
>> very little room for the introducing "conventions" like a certain
>> ordering
>> of the lengths of cell parameters. This seems to me to be a major
>> mess-up in
>> the field - a sort of "second-hand mathematics by (IUCr) committee"
>> which
>> has remained so ill-understood as to generate all these confusions. The
>> work
>> on the derivation of the classes of 4-dimensional space groups explained
>> the
>> steps of this classification beautifully (arithmetic classes ->
>> extension by
>> non-primitive translations -> equivalencing under the action of the
>> normaliser), the last step being the choice of a privileged setting *in
>> termns of the group itself* in choosing the representative of each
>> class.
>> The extra "convention" a> way
>> that depends on the metric proper

Re: [ccp4bb] problem of conventions

[Santarsiero, Bernard D.]

Ian,

I think it's amazing that we can program computers to resolve a < b < c
but it would be "a major undertaking" to store the matrix transformations
for 22121 to 21212 and reindex a cell to a standard setting. I was also
told that I was lazy to not reindex to the standard setting when I was a
grad student. Now it takes less than a minute to enter a transformation
and re-index.

The orthorhombic rule of a < b < c makes sense in 222 or 212121, but when
there is a standard setting of the 2-fold along the c-axis, then why not
adopt that? Often we chose a "non-setting" when there was a historical
precedence, as in the comparison of one structure to another, e.g., P21/c
with beta greater than 120deg vs. P21/n, etc. That is no more difficult
with modern computing than dragging along three space groups for #18.
There was a compactness to 230, and only 230 space groups. (I cheat, since
I agree there is both the rhombohedral and hexagonal cell settings for
R3bar.)

Bernie



On Thu, March 31, 2011 5:48 pm, Ian Tickle wrote:
> On Thu, Mar 31, 2011 at 10:43 PM, James Holton  wrote:
>> I have the 2002 edition, and indeed it only contains space group
>> numbers up to 230.  The page numbers quoted by Ian contain space group
>> numbers 17 and 18.
>
> You need to distinguish the 'IT space group number' which indeed goes
> up to 230 (i.e. the number of unique settings), from the 'CCP4 space
> group number' which, peculiar to CCP4 (which is why I called it
> 'CCP4-ese'), adds a multiple of 1000 to get a unique number for the
> alternate settings as used in the API.  The page I mentioned show the
> diagrams for IT SG #18 P22121 (CCP4 #3018), P21221 (CCP4 #2018) and
> P21212 (CCP4 #18), so they certainly are all there!
>
>> Although I am all for program authors building in support for the
>> "screwy orthorhombics" (as I call them), I should admit that my
>> fuddy-duddy strategy for dealing with them remains simply to use space
>> groups 17 and 18, and permute the cell edges around with REINDEX to
>> put the unique (screw or non-screw) axis on the "c" position.
>
> Re-indexing is not an option for us (indeed if there were no
> alternative, it would be a major undertaking), because the integrity
> of our LIMS database requires that all protein-ligand structures from
> the same target & crystal form are indexed with the same (or nearly
> the same) cell and space group (and it makes life so much easier!).
> With space-groups such as P22121 it can happen (indeed it has
> happened) that it was not possible to define the space group correctly
> at the processing stage due to ambiguous absences; indeed it was only
> after using the "SGALternative ALL" option in Phaser and refining each
> TF solution that we identified the space group correctly as P22121.
>
> Having learnt the lesson the hard way, we routinely use P222 for all
> processing of orthorhombics, which of course always gives the
> conventional a the pipeline and only when we are 100% confident; by that time it's
> too late to re-index (indeed why on earth would we want to give
> ourselves all that trouble?).  This is therefore totally analogous to
> the scenario of yesteryear that I described where it was common to see
> a 'unit cell' communication followed some years later by the structure
> paper (though we have compressed the gap somewhat!), and we base the
> setting on the unit cell convention for exactly the same reason.
>
> It's only if you're doing 1 structure at a time that you can afford
> the luxury of re-indexing - and also the pain: many times I've seen
> even experienced people getting their files mixed up and trying to
> refine with differently indexed MTZ & PDB files (why is my R factor so
> high?)!  My advice would be - _never_ re-index!
>
> -- Ian
>
>
>>  I have
>> yet to encounter a program that gets broken when presented with data
>> that doesn't have a> there that still don't seem to understand P22121, P21221, P2122 and
>> P2212.
>
> I find that surprising!  Exactly which 'many' programs are those?  You
> really should report them to CCP4 (or to me if it's one of mine) so
> they can be fixed!  We've been using CCP4 programs as integral
> components of our processing pipeline (from data processing through to
> validation) for the last 10 years and I've never come across one
> that's broken in the way you describe (I've found many broken for
> other reasons and either fixed it myself or reported it - you should
> do the same!).  Any program which uses csymlib with syminfo.lib can
> automatically handle all space groups defined in syminfo, which
> includes all the common alternates you mentioned (and others such as
> I2).  The only program I'm aware of that's limited to the standard
> settings is sftools (because it has its own internal space group table
> - it would be nice to see it updated to use syminfo!).
>
>> This is not the only space group convention "issue" out there!  The
>> R3x vs H3x business continues to be annoying to this day!
>
> Yeah to t

Re: [ccp4bb] problem of conventions

[Santarsiero, Bernard D.]

Interesting. My IT, both volume I and volume A (1983) only have P21212 for
space group #18. Do I have to purchase a new volume A every year to keep
up with the new conventions?

Cheers,

Bernie


On Thu, March 31, 2011 12:57 pm, Ian Tickle wrote:
>> I would like to share my experiencde with a rather unexpected problem of
>> indexing conventions. Perhaps I can save people some
>> time
>
>> I have a crystal in the more unusual P21212 space-group (No 18). Its
>> unit cell lengths are b>a>c (please note). I systematically
>> use XDS for data integration, since so far it was able to handle even
>> the most horrible-looking spots.
>
>> Now XDS indexed my data in space-group 18, but with the axes order
>> a> which does not exist. I did not realise this until I had spent a couple
>> of weeks with beautiful peaks in rotation functions, but
>> hopeless results in translation functions. It wasn't until I looked more
>> closely into the definition of the screw axes that I realised the
>> problem.
>
>> POINTLESS does not allow a reindexing of reflexions within the same
>> space-group, but fortunately REINDEX did the trick at the
>> level of intensities, because I like to use SCALA for careful scaling of
>> my data.
>
>>I was wo,dering if XDS could perhaps reindex reflexions according
>> to Int. Table conventions once the screw axes of a crystal system have
>> been
>> identified?
>
> The International Tables / IUCr / NIST convention _is_  a<=b<=c for
> orthorhombic so no re-indexing is necessary or desirable.  See IT vol.
> A 5th ed. (2002), table 9.3.4.1 (p. 758 in my edition) for all the
> conventional cells.  The problem may be that some programs are not
> sticking to the agreed convention - but then the obvious solution is
> to fix the program (or use a different one).  Is the problem that XDS
> is indexing it correctly as P22121 but calling it SG #18 (i.e. instead
> of the correct #3018).  That would certainly confuse all CCP4 programs
> which generally tend to use the space-group number first if it's
> available.
>
> I'm not clear what you mean when you say P22121 doesn't exist?  It's
> clearly shown in my edition of IT (p. 202).  Maybe your lab needs to
> invest in the most recent edition of IT?
>
> Cheers
>
> -- Ian
>

Re: [ccp4bb] problem of conventions

[Santarsiero, Bernard D.]

If you are using CCP4, it can accomodate P22121. However, just reindex in
CCP4 to the correct setting with P21212.

Bernie Santarsiero


On Thu, March 31, 2011 9:28 am, Anita Lewit-Bentley wrote:
> Dear all,
>
> I would like to share my experiencde with a rather unexpected problem
> of indexing conventions. Perhaps I can save people some time
>
> I have a crystal in the more unusual P21212 space-group (No 18). Its
> unit cell lengths are b>a>c (please note). I systematically use XDS
> for data integration, since so far it was able to handle even the most
> horrible-looking spots.
>
> Now XDS indexed my data in space-group 18, but with the axes order
> a not exist. I did not realise this until I had spent a couple of weeks
> with beautiful peaks in rotation functions, but hopeless results in
> translation functions. It wasn't until I looked more closely into the
> definition of the screw axes that I realised the problem.
>
> POINTLESS does not allow a reindexing of reflexions within the same
> space-group, but fortunately REINDEX did the trick at the level of
> intensities, because I like to use SCALA for careful scaling of my data.
>
> So, basically, beyond just warning people who might encounter similar
> problems, I was wo,dering if XDS could perhaps reindex reflexions
> according to Int. Table conventions once the screw axes of a crystal
> system have been identified?
>
> With best wishes,
>
> Anita
>
>
> Anita Lewit-Bentley
> Unité d'Immunologie Structurale
> CNRS URA 2185
> Département de Biologie Structurale & Chimie
> Institut Pasteur
> 25 rue du Dr. Roux
> 75724 Paris cedex 15
> FRANCE
>
> Tel: 33- (0)1 45 68 88 95
> FAX: 33-(0)1 40 61 30 74
> email: ale...@pasteur.fr
>
>

Re: [ccp4bb] X-Ray films

[Santarsiero, Bernard D.]

This was mentioned in Marv Hackert's outgoing remarks at the ACA meeting a
few years ago, and he showed the clip of the scene. Jimmy Stewart's
comment is apt: "It's quite fundamental. It's really odd to me that the
schools don't teach it."

Bernie


On Sun, March 27, 2011 4:13 pm, harry powell wrote:
> Yes, this is based on a Neville Shute story, stars James Stewart and
> Marlene Dietrich.
>
> James Stewart's character's daughter is "interested in
> crystallography", and her name is Elspeth (a BCA connection?)
>
> On 27 Mar 2011, at 21:04, Frances C. Bernstein wrote:
>
>> Picking up an old thread...
>>
>> Herbert and I just saw the 1951 film "No Highway in the Sky"
>> and it has several mentions of crystallography.
>>
>> 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
>> =
>
> Harry
> --
> Dr Harry Powell,
> MRC Laboratory of Molecular Biology,
> Hills Road,
> Cambridge,
> CB2 0QH
>

Re: [ccp4bb] CNS and protein structure refinement

[Santarsiero, Bernard D.]

Ditto.  YES, still generally prefer CNS v1.3 to REFMAC, especially due to
composite and simulated-annealing maps.

Different set of flagged reflections, so it might very well be different.
Also, the low-resolution solvent scaling is different between the two
refinements.

Bernie Santarsiero



On Wed, February 16, 2011 7:53 am, Boaz Shaanan wrote:
> Yes X 2
>
> Boaz
>
> - Original Message -
> From: REX PALMER 
> Date: Wednesday, February 16, 2011 15:32
> Subject: [ccp4bb] CNS and protein structure refinement
> To: CCP4BB@JISCMAIL.AC.UK
>
>> Does anyone still use CNS ?
>> Do we expect Rfree from CNS for example to be different from the
>> value given by Refmac at the end of the refinement?
>>  
>> Rex Palmer
>>  
>> Birkbeck College
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220 ; Fax: 646-1710
> Skype: boaz.shaanan‎
>

Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.

[Santarsiero, Bernard D.]

I think you should just grab a copy of Stout and Jensen, and use the
oscillation photographs directly. What's so special about a precession
image? You can still index the spots and follow along rl lines.

Bernie Santarsiero



On Thu, June 25, 2009 1:38 pm, Francis E Reyes wrote:
> Yes this is exactly what I wanted. I'm embarking on an educational
> pursuit of determining the space group from the diffraction images
> directly. Unfortunately  it seems like all the solutions insofar are
> only commercially available as part of large packages that don't list
> their prices directly on the website and, therefore, are probably too
> much for a single person to afford for just this purpose.
>
> Cheers
>
> FR
>
>
>
> On Jun 25, 2009, at 10:41 AM, Ian Tickle wrote:
>
>> But I thought what you wanted was to reconstruct the diffraction
>> pattern
>> (i.e. streaks, TDS, ice rings, zingers, warts & all) as a
>> pseudo-precession image, not just display a representation of the
>> integrated intensities.  That surely would be much more useful, then
>> one
>> could see whether the apparent systematic absence violations were just
>> streaks from adjacent spots, TDS, ice spots etc that have fooled the
>> integration algorithm.  That would be much more useful!  In the days
>> when we had real precession cameras this was how you assigned the
>> space
>> group.
>>
>> Cheers
>>
>> -- Ian
>
> -
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>

Re: [ccp4bb] coupling between occupancy and b-values in refinement

[Santarsiero, Bernard D.]

The other approach is to choose a reasonable B-factor from the atoms and
ligands in the vicinity, fix the B's, and then refine the occupancy.

It is true that the occupancy and B-factor of an atom are highly
correlated with full-matrix least-squares refinement. The only
discrimination comes from high-resolution data since the shape of the
B-factor and occupancy are different, i.e., the functional descriptions
and refinement variables are not the same, so there can be some
discrimination. This is difficult even with high-resolution small molecule
structures.

Bernie Santarsiero



On Sun, May 31, 2009 11:12 am, Poul Nissen wrote:
> If there is serious doubt of a full occupancy of the ligand and it is
> of importance for the interpreation it can in fact be handled and even
> at lower resolution (we have done it 2.8 Å resolution for PDB 2C8K for
> example) - I'm not the referee but maybe he/she is right ;-)
> You need not refine q and B at the same time, but rather just
> "titrate" q - i.e. refine the structure with fixed q changed in steps
> of 0.1 and perhaps later 0.05 -  the q that produces the most
> reasonable B-factor distribution (with ligand B comparable to
> surrounding regions) and the most clean difference map can be used.
>
> Poul
> On 31/05/2009, at 17.58, Patrick Loll wrote:
>
>> Hi all,
>>
>> I'm looking for a reference to bolster my response to a referee, in
>> which I defend my decision not to refine the occupancy of a ligand
>> in structure refined at around 2 A resolution (note the ligand
>> binding slte lies on a two-fold crystallographic axis, so the
>> maximum occupancy is 0.5)
>>
>> I recall reading a paper a LONG time ago (decades) in which someone
>> described some careful refinement experiments, and concluded that
>> the correlation between occupancy and B-value is so strong that it
>> simply makes no sense to "independently" refine both parameters (at
>> least for light atoms, and in the absence of super high resolution
>> data).
>>
>> Alas, all that I recall is this take-home message. I have no idea of
>> where the paper appeared, or the names of the authors (or indeed, if
>> I'm even remembering the paper's message correctly). I've tried
>> trolling through Acta, without success.  Does anyone have a better
>> idea of where I might find this paper, or one espousing a similar
>> message?
>>
>> Thanks,
>>
>> Pat
>>
>>
>> -
>> Patrick J. Loll, Ph. D.
>> Professor of Biochemistry & Molecular Biology
>> Director, Biochemistry Graduate Program
>> 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...@drexel.edu
>>
>>
>>
>>
>
>

Re: [ccp4bb] peak height at mouse click

[Santarsiero, Bernard D.]

Empirically, you can leave out a couple of "average" atoms in the
structure, and recalculate the maps. If you leave out a O, N, and C atom,
with relatively average B's, then you know how many electrons you should
be seeing for each in the difference map. Note that the peak height will
vary due to errors in phasing or B-factor.

Bernie Santarsiero



On Mon, April 20, 2009 11:18 am, Pavel Afonine wrote:
> Hi Thiyagarajan,
>
> the latest version of PHENIX has a command line tool called
> "phenix.real_space_correlation", that for each atom or residue computes:
>
> - map CC (where a user can define any map types, the default: 2mFo-DFc
> and Fc maps),
> - 2mFo-DFc map value at atom center,
> - mFo-DFc map value at atom center.
>
> Please let me know if you have question,
> Pavel.
>
>
> On 4/20/09 3:47 AM, S. Thiyagarajan wrote:
>> Dear CCP4 users
>>
>> Is there any easy way of calculating the peak height / number of
>> electrons at a given position, say a mouse click point in coot.
>>
>> Is there any formula to calculate the number of electrons based on
>> sigma level and peak height, as given in difference map peaks in coot.
>>
>> I have some peaks in my map which take water or sodium/magnesium or
>> chlorine atom with out giving out any positive or negative density
>> upon further refinement.
>>
>> The asymmetric unit has about 425 residues and the data resolution is
>> 1.5A.
>>
>> Thanks and regards
>>
>> S. Thiyagarajan
>> Department of Cell and Organism Biology
>> Lund University
>> Sölvegatan 35
>> Lund, Sweden
>>
>>
>

Re: [ccp4bb] Halide soaking

[Santarsiero, Bernard D.]

We were on a Br-soak flurry for awhile, and when I also talked to others,
it would work about 20-30% of the time. A few years I compared a structure
with Se-Met and native with Br-soak. There were four Br's at about 30%
occupancy, and it phased fine. It wasn't as good as the Se-Met phasing,
but we could trace and build the structure independently. It's so easy to
try that my suggestion has been to try it out first, and if it works, then
great. Also, if I had redone it, I would have soaked for longer than 20-30
seconds to try and increase the occupancy.

Bernie Santarsiero


On Tue, March 31, 2009 12:17 pm, Ethan Merritt wrote:
> On Tuesday 31 March 2009 09:57:13 Jose Antonio Cuesta-Seijo wrote:
>> Hi!
>>
>> Normally the cell parameters, etc change very very little. You'll
>> only know if the bromides got in at the synchrotron by looking at the
>> fluorescence spectrum
>
> That won't help, normally.  It only tells you that there is bromide in
> the solution, not that it found ordered positions in your crystal.
>
>> and at the anomalous signal. Normally some will
>> make it in and some will be in ordered sites, then it becomes mostly
>> a question of data quality to detect it.
>
> Right.  You have to process the data and look for a real signal.
> The mere presence of Br is not enough.
>
> In my experience, the frustrating thing is that even if the Br soak
> "works" in the sense that it introduces Br into your lattice, the
> signal is often/usually not sufficient to phase the structure
> de novo.  Nevertheless, when you eventually do solve and refine
> the structure, you can go back to your anomalous difference data
> and calculate a Bijvoet Difference Fourier that clearly shows the
> Br sites.
>
>   Ethan
>
>
>> You could also try the equivalent iodide soak. Iodine has a decent
>> anomalous signal at the copper wavenght and thus the anomalous signal
>> can be detected at your home source and many times the structure can
>> be solved by SAD or SIRAS. I would also thing that conditions that
>> give ordered iodide sites are likely to result in ordered bromide
>> sites, although the ions are not identical.
>>
>> Jose.
>>
>>
>> **
>> Jose Antonio Cuesta-Seijo
>> Cancer Genomics and Proteomics
>> Ontario Cancer Institute, UHN
>> MaRS TMDT Room 4-902M
>> 101 College Street
>> M5G 1L7 Toronto, ON, Canada
>> Phone:  (416)581-7544
>> Fax: (416)581-7562
>> email: jcue...@uhnres.utoronto.ca
>> **
>>
>>
>>
>> On Mar 31, 2009, at 12:19 PM, tat cheung cheng wrote:
>>
>> > Hi all
>> >
>> > I am now trying to do bromide soaking, but i am not really sure
>> > does the bromide atom enter my crystal. So is there any signs that
>> > indicate the entry of bromide atom? e.g. does the space group, cell
>> > dimension change? or just nothing change, and the bromide atom just
>> > get in?
>> > Thanks very much.
>> >
>> > T.C. Cheng
>> >
>> >
>> >   Yahoo!香港提供網上安全攻略，教你如何防範黑客!
>> 請前往 http://
>> > hk.promo.yahoo.com/security/ 了解更多!
>> >
>>
>>
>>
>>
>
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center
> University of Washington, Seattle 98195-7742
>

Re: [ccp4bb] X-Stream 2000 problem - ICING

[Santarsiero, Bernard D.]

We've been able to run months with an old Xstream 2000 system, so that
shouldn't be the problem. Unlike Frank, we haven't had problems with water
in the nitrogen from a nitrogen generator.

If Frank is correct, that it's water, then either the molecular sieves
need to be replaced, or there is ice buildup and blockage in the coldhead.
Usually blockage in the coldhead means that you can't get down in temp, or
can't maintain it within 1 degree or less. We do bring the temp up, run it
at RT over the weekend to dry things out, and then bring it down for
routine cooling.

If it's turbulence, then you don't have the warm and cold flow rates set
correctly. One thing you can see immediately, upon getting down to 100K,
is how far is the frosting plume from the tip of the nozzle. If you adjust
the flow rates, you can move that plume, caused by turbulence, closer or
further from the nozzle. It's also possible that there is something in the
nozzle that is causing turbulence no matter what the flow rates are, and
your vendor needs to look at that.

Bernie Santarsiero


On Mon, January 12, 2009 6:11 am, Frank von Delft wrote:
> Hi Mark
>
> We had a LOT of pain with icing, and it really comes down to one thing:
> water in the gN2.  And don't expect to measure some other way whether
> you have it, because your X-stream (or Cobra) is the most sensitive
> water meter there is.
>
> In our case, the symptom was the X-stream (and later Cobra) blocking up
> after between several days and several hours.  And we solved it by
> ditching the gN2 generators we were using, and organising boil-off gN2
> (much purer).
>
> The secondary effect of sample icing:  we'd see this as well if we had
> something (e.g. collimator) poking into the cold stream*:  that causes
> turbulence which draws in moisture.  Worst case you see ice flakes flick
> onto the crystal in real time;  best case you get an ice ball after a
> few minutes to hours.
>
> (* technically, the stationary phase between the cold and warm streams.)
>
> Hope that helps.
> phx
>
>
> Mark Agacan wrote:
>> Apologies for this slightly off topic question:
>>
>> I am having a great deal of trouble with my X-Stream 2000 cryostream
>> system and I wondered if other users have similar problems.
>>
>> I've replaced almost all components (new GAST compressors, helium
>> recharges, filters, etc., etc.) in the last couple of months but there
>> is almost always icing of any cryo within 10 - 20 minutes of mounting a
>> loop, and it is adversely affecting data collections.
>>
>> It appears like there is too much moisture in the cold or wam streams
>> but the tubes have been fully dried out as per Rigaku advice.
>>
>> This X-Stream is attached to a generator with inverted phi axis and and
>> i'm wondering if this could be the source of the problem, as the
>> X-Stream for another generator in the same laboratory with normal phi
>> axis does not ice up.  Can some sort of turbulence around the loop
>> caused by backdraft from the cryo hitting the inverted phi axis / camera
>> mount cause excess humidity and lead to icing on the pin, loop and
>> crystal?
>>
>> Has anyone else got this problem?  Any suggestions would be very
>> gratefully appreciated.
>>
>> Best Wishes,
>>
>> Mark
>>
>>
>> _
>> Dr Mark Agacan
>> Scientific Officer,
>> Division of Biological Chemistry
>> and Drug Discovery,
>> Wellcome Trust Biocentre,
>> College of Life Sciences,
>> Dow St.,
>> University of Dundee,
>> Dundee, DD1 5EH
>> Tel: +44 1382 388751
>> Fax: +44 1382 345764
>> _
>> The University of Dundee is a registered Scottish charity, No: SC015096
>>
>

[ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?

[Santarsiero, Bernard D.]

In parallel with the discussion around this off-CCP4-topic, are they any
good examples of the opposite case, where the protein is a monomer in
solution (as evident from light scattering, MW determination through
centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer?

Bernie Santarsiero

Re: [ccp4bb] Protein folding pattern schematic

[Santarsiero, Bernard D.]

PDBSum is the easiest to use for this, and some other useful information:

http://www.ebi.ac.uk/pdbsum/

Bernie

On Mon, November 10, 2008 12:34 pm, hari jayaram wrote:
> Hi CharuEspript is an excellent resource for this
> It is particulary useful when you want a secondary structure schematic
> with
> an alignment and other information relevant to the structure .. .It has a
> friendly web interface at
> http://espript.ibcp.fr/ESPript/ESPript/
>
> Fr eg
> http://espript.ibcp.fr/ESPript/ESPript/images/vp7.gif
>
> Hope this Helps
> Hari Jayaram
>
>
> On Mon, Nov 10, 2008 at 1:53 PM, Charu Chaudhry
> <[EMAIL PROTECTED]>wrote:
>
>> Hello,
>> Does anyone know of a program that can automatically generate a folding
>> pattern schematic diagram showing the arrangement of secondary structure
>> elements for a protein ? Presumably one would have to feed it a PDB file
>> with secondary structure assigned from DSSP.
>> Thanks!
>> Charu
>> Mayer lab/NIH
>>
>

Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard

[Santarsiero, Bernard D.]

My use goes back to Evans and Sutherland workstations, FRODO, SGI's with
O, Duncan's graphics program suite, and COOT, on multiple platforms.

I don't use dials at all, and multiple uses with a three-button mouse are
far more favorable.

I still prefer O to COOT for a number of reasons. The main reason is that
the graphics isn't as good on most PC/linux/mac boxes, the screen isn't as
large, and the color range isn't as good.

I rarely, if ever, use stereo options, even when available. You can in 3D
fine without it, and you need a system that has a fast enough refresh rate
and no shadowing. When users learn by building without stereo, they don't
see the advantages of it later on.

Bernie Santarsiero

>>> =>>
>>> Greetings.  This is a semi-informal survey of recent crystallography
>>> workstation users.  Please take a minute to respond.  Your answers will
>>> help us improve the crystallography computing environment.
>>>
>>>
>>> 1) Have you recently (past few months) used a crystallography
>>> workstation
>>>   for molecular model building and/or visualization?  YES  NO
>>>
>>>   Answer:  YES
>>>
>>>
>>> 2) If yes to (1), which model building software did you use (list all
>>>   that apply)?  COOT  O  
>>>
>>>   Answer:  O
>>>
>>>
>>> 3) When model building, do you use the dial box?
>>>   ALWAYS  OFTEN  SOMETIMES  RARELY  NEVER
>>>
>>>   Answer:  NEVER
>>>
>>>
>>> 4) When model building, do you use 3D stereo visualization (i.e. stereo
>>>   glasses)?  ALWAYS  OFTEN  SOMETIMES  RARELY  NEVER
>>>
>>>   Answer: RARELY to NEVER
>>>
>>>
>>> 5) If yes to (1), which molecular visualization software did you use
>>> (list
>>>   all that apply)?  COOT  O  CHIMERA  PYMOL  
>>>
>>>   Answer:  PYMOL, O, RASMOL, INSIGHT
>>>
>>>
>>> 6) When visualizing molecular models, do you use the dial box?
>>>   ALWAYS  OFTEN  SOMETIMES  RARELY  NEVER
>>>
>>>   Answer: NEVER
>>>
>>>
>>> 7) When visualizing molecular models, do you use 3D stereo
>>> visualization
>>>   (i.e. stereo glasses)?  ALWAYS  OFTEN  SOMETIMES  RARELY  NEVER
>>>
>>>   Answer: NEVER
>>>
>>>
>>> 8) Is there any software you would like to have available in the
>>>   computing environment to assist you in molecular model building
>>> and/or
>>>   visualization that is not currently available?
>>>
>>>   Answer:  NO
>>>
>>>
>>> Thank you for your time.
>>>
>>>
>>
>>
>> --
>> Dr. Jeroen R. Mesters
>> Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
>> Institut für Biochemie, Universität zu Lübeck
>> Zentrum für Medizinische Struktur- und Zellbiologie
>> Ratzeburger Allee 160, D-23538 Lübeck
>> Tel: +49-451-5004070, Fax: +49-451-5004068
>> Http://www.biochem.uni-luebeck.de
>> Http://www.iobcr.org
>> Http://www.selfish-brain.org
>> Http://www.opticryst.org
>> --
>> If you can look into the seeds of time and say
>> which grain will grow and which will not - speak then to me  (Macbeth)
>> --
>>
>>
>
>
> --
> Scott D. Pegan, Ph.D.
> Senior Research Specialist
> Center for Pharmaceutical
> Biotechnology
> University of Illinois at Chicago
>

Re: [ccp4bb] Friedel vs Bijvoet

[Santarsiero, Bernard D.]

Friedel pair is strictly F(hkl) and F(-h,-k,-l).
Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g.,
F(hkl) and F(-h,k,-l) in monoclinic.

There are always anomalous differences, though they can be unmeasurably
small.

Bernie Santarsiero

On Thu, June 26, 2008 10:55 am, Bernhard Rupp wrote:
> Dear All,
>
> I wonder about the conventions using Friedel vs Bijvoet pair.
>
> a) there are no differences. As long as h = -h, it's a Friedel
>or a Bijvoet pair. They are the same.
>
> b) A Friedel pair is any reflection h = -h including hR = -h, i.e.
>including centric reflections.
>A Bijvoet pair is an acentric Friedel pair, it can carry
>anomalous amplitude differences, whereas centric Friedel
>pairs invariably cannot. Actually, Bijvoet pairs (acentric
>Friedel pairs) invariably do carry anomalous amplitude differences.
>There is no such thing as no anomalous scattering.
>We may elect to ignore it, only.
>
> c) of course, this all assumes absence of anisotropic AS.
>
> def b) seems to be helpful in discussions and make sense given that
> absolute
>
> configuration that needs AS signal is somehow associated with
> Bijvoet's
> work.
>
> Are any authoritative answers/conventions/opinions available on that ?
>
> Thx, BR
>
> -
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> [EMAIL PROTECTED]
> [EMAIL PROTECTED]
> http://www.ruppweb.org/
> -
> The hard part about playing chicken
> is to know when to flinch
> -
>

Re: [ccp4bb] 2mhb

[Santarsiero, Bernard D.]

Bernhard,

It's complicated. The last two columns are related to atomic Z number and
group occupancy. They used a different equation than the typical
Debye-Waller equation to calculate a sort of B-factor and get the electron
density maps.

Bernie Santarsiero


On Fri, June 20, 2008 4:05 pm, Bernhard Rupp wrote:
> Dear All -
>
> can someone please explain to me the last 2 dat items in the
> 2mhb ATOM recs? Looks like X Y Z followed by B and ??
> Is this some historic legacy (1977) or another remediation incident?
> Obviousy this is not the standard format it purports to be in,
> but there might be good reasons. No access to orig citation...
>
> Thx, br
> -
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> [EMAIL PROTECTED]
> [EMAIL PROTECTED]
> http://www.ruppweb.org/
> -
> The hard part about playing chicken
> is to know when to flinch
> -
>

Re: [ccp4bb] is it Ok to freeze

[Santarsiero, Bernard D.]

Dick Dickerson tried to do the same thing at Caltech around the same time.
The major problem with cooling equipment was that the Picker goniometer
had lots of metal in it, and each of the metal pieces cooled and
contracted differently, so the alignment was always off. Nice idea, but
not useful. That's when they got the idea to just cool the sample.

Yes, Sten Samson's device was elegant in a number of ways, and we could
collect 16-20K data for weeks on it.

Bernie Santarsiero

On Thu, June 19, 2008 12:04 pm, Mischa Machius wrote:
> Ha, everyone seems to be bragging about how far back cryo-
> crystallography really goes. In that vain, I'd like to mention that,
> in Martinsried, we had a room that was lined with insulated steel
> walls and that could be flushed with liquid nitrogen. It was requested
> (demanded, really...) by Robert Huber when the Max-Planck Institute
> was finalized in 1972 (I hope I got my history right). That room
> contained an entire diffraction system. Talk about crystal cooling...
> bah, way too dinky. Cool the entire room! Of course, it was a hazard
> to work in that room, and so - as far as I know - there was only one
> post-doc from India how ever used it. That room had an ante-room with
> two more generators plus detectors that could be cooled down to -20°C!
> Ah, the good old Wild West times of macromolecular crystallography...
>
> Cheers - MM
>
>
>
> On Jun 19, 2008, at 11:48 AM, Pietro Roversi wrote:
>
>> Well everyone, talking of early applications of cryocooling to X-ray
>> crystallography, what about Sten Samson's marvellous helium cryostat
>> which was operational at Caltech since the end of the 1970s and used
>> to
>> reach temperatures around 20 K routinely , see for example:
>>
>> Proc Natl Acad Sci U S A. 1982 Jul;79(13):4040-4.
>> Structure of a B-DNA dodecamer at 16 K.
>> Drew HR, Samson S, Dickerson RE.
>>
>> That instrument (and its twin) are now both with Riccardo Destro in
>> Milano.
>>
>>  Ciao!
>>
>>  Pietro
>>
>>
>>
>>
>> --
>> Pietro Roversi
>> Sir William Dunn School of Pathology, Oxford University
>> South Parks Road, Oxford OX1 3RE, England UK
>> Tel. 0044-1865-275385
>
>
> 
> Mischa Machius, PhD
> Associate Professor
> Department of Biochemistry
> UT Southwestern Medical Center at Dallas
> 5323 Harry Hines Blvd.; ND10.214A
> Dallas, TX 75390-8816; U.S.A.
> Tel: +1 214 645 6381
> Fax: +1 214 645 6353
>

Re: [ccp4bb] is it Ok to freeze

[Santarsiero, Bernard D.]

I typically collect data at -50C on all small molecule samples. I've had
quite a few cases where there are phase transitions, and you can damage
the crystals, especially when the molecules are packed in a pi-pi stacking
motif, or I'm dealing with alloy systems.

I've also collected data at 16K, so it all depends on your sample.

Instead of finding out if there is a phase transition, -50C seems to be a
good choice of a temperature to reduce the displacement amplitudes,
radiation damage, and solvent loss.

Bernie Santarsiero


On Thu, June 19, 2008 9:40 am, Diana Tomchick wrote:
> Every small molecule dataset I collected as a graduate student in
> chemistry back in the mid to late 1980's was at 100K. I never had to
> worry about crystal slippage during collection, organic solvent
> evaporation, air oxidation of the sample (organometallic metal
> clusters) or secondary radiation damage.
>
> When I switched to protein crystallography, I was absolutely amazed
> when told that "you can not cool a protein crystal below 4 degrees C
> for data collection."
>
> How times have changed,
>
> Diana
>
> On Jun 19, 2008, at 9:03 AM, Ian Tickle wrote:
>
>> I would go along with Harry & friends, I used crystal cooling when I
>> was
>> at Aafje Vos' Struktuurchemie lab in Groningen in 1972, when the
>> technique had already been in routine use there for at least 10 years,
>> in order to study compounds that are liquid at ambient temp (of course
>> it was custom-built kit using a collection of liq N2 Dewar vessel &
>> tubes, nothing as fancy as a Cryostream!).  The Groningen group really
>> pioneered the use of low temp for small molecule structures and I
>> don't
>> recall increased mosaicity ever being an issue.  Occasionally you
>> would
>> get a compound with a phase transition on the way down and the crystal
>> would literally explode in a puff of powder before your eyes!  The
>> motive for using low temp was of course to reduce the thermal motion
>> and
>> libration effects, and thus greatly improve the accuracy of the
>> molecular geometry, and low temp is pretty well essential if you're
>> into
>> valence density deformation maps, again in order the minimise the
>> contribution from thermal motion.
>>
>> -- Ian
>>
>>> -Original Message-
>>> From: [EMAIL PROTECTED]
>>> [mailto:[EMAIL PROTECTED] On Behalf Of harry powell
>>> Sent: 19 June 2008 14:05
>>> To: Remy Loris
>>> Cc: CCP4BB@JISCMAIL.AC.UK
>>> Subject: Re: [ccp4bb] is it Ok to freeze
>>>
>>> Hi
>>>
>>> Without wishing to start an argument, I've been checking with
>>> some of my colleagues who are chemical crystallographers -
>>> the reply I get is that, for routine structural analysis,
>>> "pretty well all datasets are collected at 100K unless the
>>> crystals fall apart at low T, or if the cryostream is broken".
>>>
>>> I should point out that the first production Cryostream that
>>> I came across (serial number 2, which I think may have been
>>> the first one sold!) was in the Cambridge Department of
>>> Chemistry in about 1985. They didn't become common until the
>>> mid-1990's in PX labs, when they were already
>>> well-established as a bit of pretty well essential kit for
>>> small molecule work.
>>>
>>> So although what Remy says is true, the practice is to
>>> cryocool most of the time.
>>>
>>>
>>> On 19 Jun 2008, at 12:08, Remy Loris wrote:
>>>
>>>
>>> Typically crystals of small organic compounds do not
>>> require freezing as there are no solvent channels. They do in
>>> general not suffer from radiation damage at room temperature
>>> the way protein crystals do. Occasionally they are mounted in
>>> a capillary instead of simply glueing them to a goniometer if
>>> they are air sensitive. In principle freezing should not
>>> damage the crystals, but one still may have to be carefull if
>>> the crystals are large. I think you risk increasing
>>> mosiacity, and any manipulation that is not needed will on
>>> average only reduce the quality of the specimen rather than improve
>>> it
>>>
>>> Remy Loris
>>> Vrije Univesiteit Brussel
>>>
>>> Jayashankar wrote:
>>>
>>> Dear Scientists and Friends,
>>> I am not sure, whether  organic crystals  need
>>> to be in cryo stream necessarily during data  collection from
>>> an  in house
>>> xray machine .
>>> How most of the organic crystals have been
>>> solved mostly?
>>> --
>>> S.Jayashankar
>>> (A bit confused new generation researcher).
>>> Research Student
>>> Institute for Biophysical Chemistry
>>> Hannover Medical School
>>> Germany
>>>
>>>
>>> Harry
>>> --
>>> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC
>>> Centre, Hills Road, Cambridge, CB2 2QH
>>>
>>>
>>>
>>>
>>>
>>
>>
>> Disclaimer
>> This communication is confidential and may contain privileged
>> information intended solely for the named addressee(s). It may not
>> be used or disclosed e

Re: [ccp4bb] heavy atom derivative(s) for tutorial

[Santarsiero, Bernard D.]

Depending on your time, I'd recommend adding the use of a native gel band
shift to try a one that doesn't work and one that does.

http://www.doe-mbi.ucla.edu/~sawaya/m230d/Crystallization/crystallization.html

I know you can use NaBr or NaI to grow lysozyme crystals as well, and they
stick on hydrophobic patches of the enzyme's surface. I do recall,
however, that the crystal system changes from tetragonal to the triclinic
or monoclinic forms.

Bernie




On Fri, April 11, 2008 8:09 am, Patrick Loll wrote:
> Hi,
>
> Does anyone have a foolproof recipe for preparing one or more heavy
> atom derivatives for a nice, easily crystallized protein like
> lysozyme?  I'm looking for something that I can use as a hands-on MIR/
> SIR tutorial for beginning students. I'd rather the students be able
> to focus their attention on data collection and analysis, rather than
> spending a lot of time screening different soaks.
>
> I have looked at Peter Sun's paper on quick soaking (Acta Cryst D58:
> 1092-1098, 2002), and will definitely try what they did; but any
> other recipes would also be welcome.
>
> Thanks,
>
> Pat
>
>
> 
> ---
> Patrick J. Loll, Ph. D.
> Professor of Biochemistry & Molecular Biology
> Director, Biochemistry Graduate Program
> 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
> [EMAIL PROTECTED]
>
>

Re: [ccp4bb] Model ensemble for x-ray crystallography

[Santarsiero, Bernard D.]

On Fri, March 28, 2008 10:13 am, Lucas Bleicher wrote:
> Some time ago I've heard about the idea of proposing
> an ensemble of models (as in NMR), instead of a single
> model for x-ray crystallography structures. If I
> remember correctly, this idea has been published
> somewhere. Can anyone tell me what article is that?
>
> Lucas
>
>
>   Abra sua conta no Yahoo! Mail, o único sem limite de espaço para
> armazenamento!
> http://br.mail.yahoo.com/
>


The earliest I recall hearing about this from was W. F. van Gunsteren,
where he used an ensemble average of ten chains instead of a a single atom
chain with anisotropic Gaussian displacement parameters. Check out:

P. Gros, M. Fujinaga, B. W. Dijkstra, K. H. Kalk, and W. G. J. Hol, Acta
Cryst., B45, 488-499 (1989)

Bernie

Re: [ccp4bb] XDS and overlaps

[Santarsiero, Bernard D.]

I use XDSCONV to make the mtz file using all of the reflections. Then I
use uniqueify in CCP4 to make sure the asymmetric unit is correct for
CCP4, and tag the test set.

Bernie Santarsiero


On Thu, February 21, 2008 9:32 am, Dirk Kostrewa wrote:
> Usually, I run CAD first after F2MTZ to make sure that the
> reflections are in the correct reciprocal asymmetric unit for CCP4
> programs. I think, UNIQUE on its own doesn't do this, but the
> UNIQUEIFY script calls CAD, UNIQUE and FREERFLAG for setting a
> FreeR_flag column. The latter may or may not be wanted, depending on
> whether the test-set has been assigned by XDS/XSCALE, already.
>
> Best regards,
>
> Dirk.
>
> Am 21.02.2008 um 16:15 schrieb [EMAIL PROTECTED]:
>
>> In my experience when going from XDS via some intermediate file to
>> mtz format, XDS uses in some cases a different reciprocal
>> asymmetric unit as mtz uses, which may result in only half of the
>> reflections being used and/or ccp4 programs getting confused. By
>> using UNIQUE, one makes sure that the reflections are mapped to the
>> correct asymmetric unit. It has nothing to do with missing
>> reflections but is in many cases essential.
>>
>> Best regards,
>> Herman
>>
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf
>> Of Kay Diederichs
>> Sent: Thursday, February 21, 2008 3:46 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] XDS and overlaps
>>
>> Simon Kolstoe schrieb:
>>> Whilst we are on the subject of XDS...
>>>
>>> I had difficulty processing a data-set in mosflm the other day so on
>>> the recommendation of a colleague switched to xds which, with a
>>> bit of
>>> tweaking, seemed to work really well. I converted the resulting
>>> XDS_ASCII.HKL using xdsconv and then f2mtz ready for phaser and
>>> refmac.
>>
>> We do it in the same way here.
>>
>>>
>>> However, my colleague then told me that xds handled missing
>>> reflections differently from the usual mosflm/CCP4 route
>>
>> I have honestly not the slightest idea what your colleague was
>> referring to.
>>
>>> and thus I had to run the CCP4 program UNIQUE before I tried
>>> refinement as apparently refmac does not like reflection files
>>> originally processed with xds. As I couldn't
>>
>> In the case of a new project, one should run "uniqueify" or some
>> other means of assigning reflections to the free set (thin shells
>> come to mind; see earlier discussions on CCP4BB).
>>
>> In the case of an old project, one should transfer the free set of
>> reflections from some master data set to the new dataset.
>>
>> None of this is specific to XDS.
>>
>> HTH,
>>
>> Kay
>>
>>> find anything in the literature about this I was wondering whether
>>> this advice is still up to date?
>>>
>>> Thanks,
>>>
>>> Simon
>>>
>>>
>>> On 21 Feb 2008, at 09:44, Kay Diederichs wrote:
>>>
 Engin Ozkan schrieb:
> Hi everyone,
> I have been recently relying on XDS quite a bit, but at the same
> time worrying about how XDS treats overlaps.  We had one dataset
> that both HKL2000 and Mosflm would show to have severe overlaps, as
> expected due to unit cell parameters and the unfortunate crystal
> orientation in the loop. We always ended up with completeness
> percentages in the 70's.
> XDS can find the same lattice, index and scale the data, but yields
> a 100% complete mtz (and a nice structure). Without the
> HKL/Mosflm-like GUI, it is difficult to assess the fate of the
> overlapped observations in XDS. What I could see with VIEW was that
> some observations were being divided into several ovals, probably
> different reflections, but I'm not very certain.
> So, the basic question is, how does XDS treat overlaps?  I could
> not
> find in the documentation an answer to this question; the single
> mention of overlaps I could find tells me that XDS can recognize
> overlaps, but does not tell me if it rejects them, or divvies them
> up into separate reflections, and if that is the case, how does it
> divide them, and how reliable is that? Depending on how it divides
> the overlaps, could that affect commonly-used intensity stats and
> distributions?
> Thanks,
> Engin

 Engin,

 the basic answer is:
 a) each pixel of the detector is assigned to its nearest reflection
 in reciprocal space
 b) some of these pixels will mostly allow the background estimation,
 others will mostly contribute to the integration area (but as they
 are transformed into a local coordinate system there is not a 1:1
 relationship). At this step, pixels which should be background but
 are higher than expected (due to overlap) are rejected.
 c) for each reflection, the background is estimated, and the 3D
 profile is assembled from the pixels contributing to it
 d) a comparison is made: for a reflection, is the percentage of its
 observed profile assembled in c) larger than so

Re: [ccp4bb] XDS and overlaps

[Santarsiero, Bernard D.]

The only other comment that I'd add is XDS builds real three-dimensional
profiles, whereas HKL2000 uses two-dimensional profiles. Thus, you can
imagine that if you have already defined a 3D profile, XDS only needs part
of the reflection, over one or more images, to estimate the overall
intensity of a reflection. This is still possible with 2D profiling, but
you can imagine that overlapping reflections over more than one image may
be more problematic for an estimation of the reflection.

Bernie Santarsiero


On Thu, February 21, 2008 3:44 am, Kay Diederichs wrote:
> Engin Ozkan schrieb:
>> Hi everyone,
>>
>> I have been recently relying on XDS quite a bit, but at the same time
>> worrying about how XDS treats overlaps.  We had one dataset that both
>> HKL2000 and Mosflm would show to have severe overlaps, as expected due
>> to unit cell parameters and the unfortunate crystal orientation in the
>> loop. We always ended up with completeness percentages in the 70's.
>>
>> XDS can find the same lattice, index and scale the data, but yields a
>> 100% complete mtz (and a nice structure). Without the HKL/Mosflm-like
>> GUI, it is difficult to assess the fate of the overlapped observations
>> in XDS. What I could see with VIEW was that some observations were being
>> divided into several ovals, probably different reflections, but I'm not
>> very certain.
>>
>> So, the basic question is, how does XDS treat overlaps?  I could not
>> find in the documentation an answer to this question; the single mention
>> of overlaps I could find tells me that XDS can recognize overlaps, but
>> does not tell me if it rejects them, or divvies them up into separate
>> reflections, and if that is the case, how does it divide them, and how
>> reliable is that? Depending on how it divides the overlaps, could that
>> affect commonly-used intensity stats and distributions?
>>
>> Thanks,
>>
>> Engin
>
> Engin,
>
> the basic answer is:
> a) each pixel of the detector is assigned to its nearest reflection in
> reciprocal space
> b) some of these pixels will mostly allow the background estimation,
> others will mostly contribute to the integration area (but as they are
> transformed into a local coordinate system there is not a 1:1
> relationship). At this step, pixels which should be background but are
> higher than expected (due to overlap) are rejected.
> c) for each reflection, the background is estimated, and the 3D profile
> is assembled from the pixels contributing to it
> d) a comparison is made: for a reflection, is the percentage of its
> observed profile assembled in c) larger than some constant (called
> "MINPK" in XDS.INP)? If the answer is no, this reflection will be
> discarded (you could call this situation "overlap").
>
> Among other things, this means that:
> a) the program does _not_ look around each reflection to detect an
> overlap situation, it just tries to gather the pixels for each reflection
> b) as a user, when your crystal-detector distance was chosen too low or
> the reflections are very broad (resulting in generally strong overlap),
> you may reduce MINPK down to 50. This will result in more completeness,
> but you should monitor the quality of the resulting data. Conversely, if
> you raise MINPK over its default of 75 you will discard more
> reflections, but the resulting dataset will be a bit cleaner.
>
> The reference is
> W. Kabsch (1988)  Evaluation of single-crystal X-ray diffraction data
> from a position-sensitive detector. J. Appl. Cryst. 21, 916-924.
> (http://dx.doi.org/10.1107/S0021889888007903)
>
> HTH,
>
> Kay
> --
> Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
> email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>

Re: [ccp4bb] differences between Rsym and Rmerge

[Santarsiero, Bernard D.]

Ed,

You don't need to adjust them in XDS.

In scalepack, I don't adjust the individual chi^2's (the additive terms,
by shell), but I do adjust the multiplier to get the chi^2's in the
highest resolution shell, usually with  (or /) ~ 1, to be
near and greater than 1.0. Then the overall chi^2's are what they are. My
rationale is that the weakest shell will be dominated most by random
errors, and should approach 1.0, whereas the lower resolution shells
typically have chi^2's greater than 1, and are dominated by systematic
(absorption, misalignment, integration) errors. If they aren't close to 1,
then that's telling you something, whether or not the R(sym) is.

I report the overall chi^2 and the value in the highest resolution shell,
and they're in the pdb/cif file.

Bernie

On Fri, January 18, 2008 2:28 pm, Edwin Pozharski wrote:
> Bernie,
>
> but my chi-squares are always near 1.0, so why would I report it?  How
> close they should be to 1 is open to discussion, of course.   The point
> is, it is assumed (at least in scalepack) that you adjust your error
> model until chi-square~1.  I have never seen a statistics table in a
> paper which would report chi-suqares.
>
> I am afraid I may be misinterpreting what you were trying to say - I
> apologize if that is the case.
>
> Cheers,
>
> Ed.
>
> Santarsiero, Bernard D. wrote:
>> You know there is that other funny column with chi^2's. I like to quote
>> both. Half of the reviewers will know which column to look at, but you
>> will satisfy the other half.
>>
>> Bernie
>>
>> On Fri, January 18, 2008 1:39 pm, Edwin Pozharski wrote:
>>
>>> There are two opposing views on this.
>>>
>>> First:  Rmerge doesn't matter.  Don't even look into that column in
>>> scalepack output, you will be upset over nothing.  If you collect twice
>>> as much data (360 sweep instead of 180) from the same crystal, your
>>> Rmerge will go up due to higher redundancy, but the dataset will
>>> actually get better because you measuring every reflection twice more
>>> and your I/sigma will increase by ~40%.
>>>
>>> Second:  Rmerge is very important, because if it is, say, 100% (oh,
>>> those zeros in the scalepack output) it means that symmetry-related
>>> reflections vary by about 100%, so your data is a pile of garbage (at
>>> least in that resolution shell).  Cut your data at the resolution where
>>> Rmerge is 30% and you will be rewarded by really low Rfactors for your
>>> final model.  Plus, if you keep all the data to where I/sigma~1, your
>>> Rmerge is guaranteed to be 0.00 in the output, and what are you going
>>> to
>>> tell reviewers of your paper?
>>>
>>> Of course, truth is somewhere in the middle.  If I collect on two
>>> crystals of the same type (assuming everything else is the same, such
>>> as
>>> redundancy), and one has much higher Rmerge, then I should probably
>>> choose the other one.  If you cut resolution at I/sigma~1, and your
>>> overall Rmerge is about 10%, I think it's normal.  But if it's 30%, you
>>> may have some unusually high level of noise in your data (satellite
>>> crystal?  twinning?  evil xray fairy messing with you?).  So Rmerge
>>> does
>>> tell you something, but only in context with all the other information.
>>> After all, the only thing that matters is if your electron density map
>>> is interpretable.  I dare to say that the quality of the map you get
>>> does correlate with Rmerge, but would I discard a dataset just because
>>> Rmerge is high without trying to solve the structure and take a look at
>>> the density?  Never.
>>>
>>> Cheers,
>>>
>>> Ed.
>>>
>>> Mischa Machius wrote:
>>>
>>>> OK, that brings us back to a more substantial question: is any of
>>>> these R values actually suitable to judge the quality of a given
>>>> dataset? Instead of introducing novel R factors, one could also simply
>>>> ignore them altogether, make sure that the error models have been
>>>> properly chosen and look at I/sigma(I) as the main criterion. [QUOTE
>>>> ]If anyone then still wants to present low R factors, one can always
>>>> divide by 2, if necessary. [/QUOTE]
>>>>
>>>> Best - MM
>>>>
>>>>
>>>> On Jan 18, 2008, at 1:02 PM, Salameh, Mohd A., Ph.D. wrote:
>>>>
>>>>
>>>>> Thank you all, it was very, very helpful discussion. However, I
>>>>

Re: [ccp4bb] differences between Rsym and Rmerge

[Santarsiero, Bernard D.]

You know there is that other funny column with chi^2's. I like to quote
both. Half of the reviewers will know which column to look at, but you
will satisfy the other half.

Bernie

On Fri, January 18, 2008 1:39 pm, Edwin Pozharski wrote:
> There are two opposing views on this.
>
> First:  Rmerge doesn't matter.  Don't even look into that column in
> scalepack output, you will be upset over nothing.  If you collect twice
> as much data (360 sweep instead of 180) from the same crystal, your
> Rmerge will go up due to higher redundancy, but the dataset will
> actually get better because you measuring every reflection twice more
> and your I/sigma will increase by ~40%.
>
> Second:  Rmerge is very important, because if it is, say, 100% (oh,
> those zeros in the scalepack output) it means that symmetry-related
> reflections vary by about 100%, so your data is a pile of garbage (at
> least in that resolution shell).  Cut your data at the resolution where
> Rmerge is 30% and you will be rewarded by really low Rfactors for your
> final model.  Plus, if you keep all the data to where I/sigma~1, your
> Rmerge is guaranteed to be 0.00 in the output, and what are you going to
> tell reviewers of your paper?
>
> Of course, truth is somewhere in the middle.  If I collect on two
> crystals of the same type (assuming everything else is the same, such as
> redundancy), and one has much higher Rmerge, then I should probably
> choose the other one.  If you cut resolution at I/sigma~1, and your
> overall Rmerge is about 10%, I think it's normal.  But if it's 30%, you
> may have some unusually high level of noise in your data (satellite
> crystal?  twinning?  evil xray fairy messing with you?).  So Rmerge does
> tell you something, but only in context with all the other information.
> After all, the only thing that matters is if your electron density map
> is interpretable.  I dare to say that the quality of the map you get
> does correlate with Rmerge, but would I discard a dataset just because
> Rmerge is high without trying to solve the structure and take a look at
> the density?  Never.
>
> Cheers,
>
> Ed.
>
> Mischa Machius wrote:
>> OK, that brings us back to a more substantial question: is any of
>> these R values actually suitable to judge the quality of a given
>> dataset? Instead of introducing novel R factors, one could also simply
>> ignore them altogether, make sure that the error models have been
>> properly chosen and look at I/sigma(I) as the main criterion. [QUOTE
>> ]If anyone then still wants to present low R factors, one can always
>> divide by 2, if necessary. [/QUOTE]
>>
>> Best - MM
>>
>>
>> On Jan 18, 2008, at 1:02 PM, Salameh, Mohd A., Ph.D. wrote:
>>
>>> Thank you all, it was very, very helpful discussion. However, I
>>> collected crystal data and the Rmerge overall was very high around 0.17
>>> at 2.6A resolution and I'm wondering what is the acceptable value
>>> (range) of R-merge that worth the time to continue processing! Very
>>> anxious to hear your thoughts. Thanks, M
>>> 
>>> Mohammed A. Salameh, Ph.D.
>>> Mayo Clinic Cancer Center
>>> Griffin Cancer Research Building
>>> 4500 San Pablo Road
>>> Jacksonville, FL 32224
>>> Tel:(904) 953-0046
>>> Fax:(904) 953-0277
>>> [EMAIL PROTECTED]
>>> 
>>>
>>>
>>> -Original Message-
>>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
>>> Chris Putnam
>>> Sent: Friday, January 18, 2008 1:21 PM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: Re: [ccp4bb] differences between Rsym and Rmerge
>>>
>>> On Friday 18 January 2008 09:30:06 am Ethan A Merritt wrote:

 Rmerge is an average over replicate measurements of the intensity for
 identical [hkl]. Rsym is an average over the measurements for all
>>> symmetry
 equivalent reflections.

 In the presence of anomalous scattering, Rsym will be higher than
>>> Rmerge
 because the Bijvoet pairs, although symmetry related, do not have
>>> identical
 intensities.

 One might logically report two values for Rsym,  one which averages
 over the Bijvoet-paired reflections and one which does not.

>>>
>>> This has been an eye-opening discussion for me.  I've been really
>>> surprised
>>> that there's been such a diversity of opinion about what these common
>>> terms ought to refer to, and the fact that my understanding was wrong.
>>> I always thought that Rsym was an average over all symmetry equivalent
>>> reflections from the same crystal (including Bijvoet pairs) and Rmerge
>>> was
>>> properly restricted to cases of multi-crystal averaging.  (My versions
>>> of
>>> Table 1's from single crystals have used "Rsym" rather than "Rmerge".)
>>>
>>> I wonder if the problem here is that the terms have become overloaded
>>> (and
>>> hence non-specific).  In that sense "Rmerge" is a particularly
>>> unfortunate
>>> name as every R that we're discussing is a real

Re: [ccp4bb] differences between Rsym and Rmerge

[Santarsiero, Bernard D.]

I seem to recall hearing Rsym first when I used the Xuong-Hamlin detector,
since there were a substantial number of redundancies. There were two
Rsyms, one called Rrms for the sqrt over the sum of weighted squared
differences and and Rav for the linear summation of unweighted
differences. This was for protein work.

I do recall Rmerge being more popular with the small molecule
crystallographers. However, I also recall a difference between averaging
over pairs of reflections that were or were not Bijvoet pairs, for even
small differences in the anomalous scattering contributions.

Bernie



On Fri, January 18, 2008 9:29 am, R.M. Garavito wrote:
> Kay,
>
> I beg to differ, but only in a pedantic way.  Historically, Rsym
> would refer to the agreement in symmetry-related reflections within a
> single data set and Rmerge would be the agreement between 2 or more
> data sets that were merged.  This was the way we did it back in the
> "old day" of precession photography and early oscillation
> photography.  While the terms seem synonymous today, the recent
> thread "[ccp4bb] combine incomplete data sets" illustrates where such
> a distinction is still relevant, where the "merging" is between data
> collected under different experimental conditions (i.e., a different
> crystal in a different orientation).
>
> Michael
>
> 
> R. Michael Garavito, Ph.D.
> Professor of Biochemistry & Molecular Biology
> 513 Biochemistry Bldg.
> Michigan State University
> East Lansing, MI 48824-1319
> Office:  (517) 355-9724 Lab:  (517) 353-9125
> FAX:  (517) 353-9334Email:  [EMAIL PROTECTED]
> 
>
>
> On Jan 18, 2008, at 10:15 AM, Kay Diederichs wrote:
>
>> Salameh, Mohd A., Ph.D. schrieb:
>>> Hi everybody!
>>> I will appreciate it if anybody can clarify to me the differences
>>> between Rmerge and Rsym. Many thanks, M
>>
>> there is no difference - unfortunately there are two words for the
>> same thing. "Rmerge" currently appears to be more in fashion.
>>
>> just my 2 cents,
>>
>> Kay
>> --
>> Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
>> email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>
>

Re: [ccp4bb] crystallisation robot

[Santarsiero, Bernard D.]

In our original work on a prototype, we used the Cartesian technology. We
were able to dispense 10nL+10nL drops with a large range of viscosities
without difficulty. The main issue was to wash the tips after use to
prevent clogging. That was with a system that could dispense 1nL droplets.
The present systems are sub-nL now. We didn't have a problem with
electrostatics.

More recently, I've looked at all of the crystallization robot vendors.
For single lab users, all of the systems work well. Systems like the Hydra
or Mosquito are less automatic, but provide the basic functions for
crystallization trial setup. For more of a user facility with a large
number of users from several groups, you want more automation to avoid
protocols that can damage the components, like alignment or breakage of
the needles. You also want to consider the total annual cost of
expendables and maintenance.

Bernie Santarsiero

On Wed, January 16, 2008 5:46 am, Demetres D. Leonidas wrote:
> Oryxnano 50+50 nL
>
> Demetres
>
>
> David Briggs wrote:
>> I'll defend the honour of the phoenix... (again)
>> Bernhard Rupp 100+100 nl
>> Dave Briggs (and all users at Univ of Manchester, UK) 100+100nl Others..
>> Only time we have ANY problems is when the nano dispensing tip gets
clogged. Often a good wash whilst still on the machine will clear the
blockage.
>> Dave
>> --
>> 
>> David C. Briggs PhD
>> Father & Crystallographer
>> http://www.dbriggs.talktalk.net  AIM
ID: dbassophile
>> 
>
> --
> Demetres D. Leonidas, Ph.D.
> Structural Biology & Chemistry Group
> Institute of Organic and Pharmaceutical Chemistry
> The National Hellenic Research Foundation
> 48, Vassileos Constantinou Avenue
> Athens 116 35, Greece
> ==
> Tel. +30 210 7273841 (office)
>  +30 210 7273895 (lab)
> Fax. +30 210 7273831
> E-mail: [EMAIL PROTECTED]
> URL: http://athena.eie.gr
> ==
>

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

[Santarsiero, Bernard D.]

I would also ask what is the actual goal in refining the occupancy of the
ligand?

While I agree wholeheartedly with George, the B-factors will adequately
model a lower ligand occupancy.  Usually the question you want to resolve
is "Is the ligand really bound in the active site, or is this an artifact
of the model?"  However, if you're trying to resolve a static disorder in
an active site, say half ligand and half solvent occupancies, then
refining the ligand occupancy can be useful.

Thus, what you really need to do is compare a refinement with just
B-factors and full occupancies vs. a refinement with the added restrained
ligand occupancy variable, in some sort of R-test, comparison of GOF, etc.
Does it really improve the model?

Bernie Santarsiero

On Mon, December 17, 2007 8:43 am, George M. Sheldrick wrote:
> I thought that I would never have to disagree with both Eleanor and
> Tassos in the same email, let alone risk being burnt at a stake as a
> heretic for doubting the Gospel according to Kleywegt, but in my
> experience, given the very fortunate position that you have data to
> 1.5A, the refinement of one occupancy parameter for the whole ligand
> (e.g. one SHELX free variable) will be rather well defined provided
> that sensible restraints are applied to the B-values. A common variant
> of this for ligands or side-chains is to refine one component with
> occupancy p and an alternative component or conformation with an
> occupancy 1-p, still only requiring the addition of ONE refinable
> parameter. If you are using SHELX and your ligand (or part of it)
> happens to be rigid, the rigid group refinement offers a further
> way of keeping the number of refinable parameters down. The Dundee
> PRODRG server is an excellent source of ligand geometries and
> restraints for such refinements.
>
> 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. +49-551-39-2582
>
>
> On Mon, 17 Dec 2007, Anastassis Perrakis wrote:
>
>> > I have already changed occupancies as Eleanor mentioned, and got
>> > approximate values. But my hope is to try to get much precise ones if
>> > possible.
>> >
>> I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
>> but in this case what you need is more accurate answers, not more
>> precise ones
>> (or better both, but precision alone can be a problem, and you can
>> easily get
>> 'precise' but inaccurate data easily by making the wrong assumptions
>> in your experiment)
>>
>> http://en.wikipedia.org/wiki/Accuracy
>>
>> > I have heard from my colleague SHELX can refine occupancies, and
>> > got its license. I'll next try SHELX.
>>
>> I think that phenix.refine can also do occupancies ?
>> The problem is not  if the program can do it, but if at your specific
>> case
>> you have enough information to do that in a meaningful way.
>>
>> For a soaking experiment and 1.5 A data, I would say that Eleanor's
>> suggestion
>> of tuning Occ based on B, is as close as you would get, accurate enough
>> given
>> the data,
>> although not necessarily too precise.
>>
>> Tassos
>>
>

Re: [ccp4bb] To bathe or not to bathe.

[Santarsiero, Bernard D.]

The main reason was related to absorption. If you didn't completely bathe
the crystal in the xray beam, then the diffracting volume of the crystal
would be different during the data collection, and thus, scaling would be
inaccurate, especially when there was radiation damage. This was
especially true when you weren't sure that the crystal was well-centered
in the xray beam (in a cryostat, and therefore not visible). We typically
collected highly redundant data to help compensate for this. We also used
to correct for absorption by assigning Bragg indices to the crystal and
making precise measurements of crystal dimensions.

Scaling programs are now more extensive, and include options to calculate
a pseudo-absorption surface. In principle, if you have a beam that is
ALWAYS smaller than the crystal, then the same crystal volume is
illuminated by the xray beam, and will minimize scaling errors.

Bernie Santarsiero



On Fri, November 23, 2007 4:34 pm, Jim Pflugrath wrote:
> It probably goes back to the days of using a single-counter diffractometer
> where one didn't have multiple Bragg reflections on an image or film pack.
> That is, each reflection was collected by itself.  Even in a small
> molecule
> crystal data collection nowadays, it would not hurt to have the crystal
> completely bathed in the beam.
>
> Also in the old days (let's say pre-cryo), there was plenty of radiation
> damage going on even with a sealed-tube source.  We always corrected for
> radiation damage by extrapolating back to zero dose in those days.
>
> Jim
>
> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
> Robert
> Sweet
> Sent: Friday, November 23, 2007 4:08 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] To bathe or not to bathe.
>
> Jorge,
>
> You said,
>
>>   I remember one former good (small molecule ?) crystallography book
>> with words a kind of this "the crystals should be completely bathed by
>> the x-ray beam during the whole data collection"  ...
>
> The original motive for bathing the whole crystal was to assure that the
> relative intensity of the data on each successive film pack was very
> nearly constant.  This was possible (one might say "necessary") in the old
> days because the laboratory sources were very stable and the intensity was
> low enough that there wasn't a lot of x-ray damage to the crystals.
> There were a couple of other good reasons to pay attention to details like
> this.  One was that methods for scaling images together were not quite as
> good as now, and another was that film data were relatively very much less
> accurate than what is achievable now with excellent detectors and brighter
> sources.  To combat all of that, we tried to do everything possible to
> make things better.
>
> These days scaling algorithms are good, the detectors are excellent, and
> very often it pays to employ a beam smaller than the x-tal.  This, the
> non-uniformity of many synchrotron beams, and the systematic damage
> to crystals that we observe now with synchrotron sources cause serious
> systematic errors.  We're forced to depend on good scaling and good
> detectors to get accurate measurements.  Making the measurements in many
> different crystal orientations (redundancy) helps to smooth out these
> systematic errors.
>
> Nonetheless, it will always pay you to watch for EACH of these sources of
> error and to minimize them as best you can.
>
> Bob
>
> =
>  Robert M. Sweet E-Dress: [EMAIL PROTECTED]
>  Group Leader, PXRR: Macromolecular   ^ (that's L
>Crystallography Research Resource at NSLSnot 1)
>http://px.nsls.bnl.gov/
>  Biology Dept
>  Brookhaven Nat'l Lab.   Phones:
>  Upton, NY  11973631 344 3401  (Office)
>  U.S.A.  631 344 2741  (Facsimile)
> =
>

Re: [ccp4bb] difference of R_work and R_free as a function of resolution

[Santarsiero, Bernard D.]

One of the major problems with any R-factor is that it's a function of the
denominator, and therefore I, F^2, or F. Depending on how you "push" to
higher resolution, the R's will very likely increase due to the dominance
of the denominator over the numerator. It's good to also monitor on
evaluation functions that follow the numerator, like chi^2 in
scaling/averaging, and the figure-of-merit (rho-calc vs. rho-obs), and
goodness-of-fit.

Bernie Santarsiero

On Thu, November 15, 2007 10:41 am, Kay Diederichs wrote:
> Dear crystallographers,
>
> today I explained to a student that I believe that the difference of
> R_work and R_free should decrease as a function of resolution, because
> at high resolution there is less danger of overfitting, whereas at low
> resolution one is always overfitting to some extent. I'd say this should
> be true at least in absolute terms, but probably even in relative terms:
> for example, for a 1.5A structure I'd expect R_work/R_free= 14%/16%,
> whereas at 3A I'd expect 28%/35%.
>
> I believe that I saw plots (maybe in a link given in a posting on
> CCP4BB) obtained for structures from the PDB, which confirmed this
> hypothesis. But I've been googling and searching through postings now
> for quite some while, and cannot seem to find anything to that effect.
>
> Does anybody have a pointer to an analysis of this effect?
>
> thanks,
>
> Kay
>
> P.S. Would be good to put this into the CCP4 Wiki article on R-factors
> --
> Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
> email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>

Re: [ccp4bb] Wavelength of Copper Kalpha

[Santarsiero, Bernard D.]

On Wed, October 10, 2007 11:50 am, Bryan W. Lepore wrote:
> On Wed, 10 Oct 2007, Jim Pflugrath wrote:
>> It has come to my attention that the wavelength of a Copper Kalpha may
>> have changed over the years.  At least this appears to be true if you
>> look at the International Tables.
>
> the 'natural' isotopic distribution must have changed, as it has with the
> biggest example lithium, since the 'nuclear age' - i take that to be the
> principal reason.
>
> and i take it that everyday-use copper anodes are isotopically impure?
>
> -bryan
>
The change was probably around 1967, when the meter was defined, slightly,
using krypton. Tungsten was used as a reference, and the kX to A ratio was
changed: Bearden, Rev Mod Phys, 39, 78 (1967).

old values from IT, volume III
alpha-1 1.54051
alpha-2 1.54433
beta-1  1.39217
beta-2  1.38102

alpha   1.54178

the ratio of I(alpha-2)/I(alpha-1) = 0.497
the units are kX/1.00202, and good to 1 in 25,000, based on kX, for 1962
(IT, 1962).

newer values, from IT, volume IV

alpha-1 1.540562
alpha-2 1.544390
beta-1  1.392218
beta-5  1.38109

based on the W K-alpha-1 line/peak at 0.2090100 A

Bernie Santarsiero

Re: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds

[Santarsiero, Bernard D.]

My usual targets are 0.010 for the bonds and 1.50 for the angles.

Bernie Santarsiero


On Tue, September 11, 2007 3:22 pm, Lari Lehtio wrote:
> Hello!
>
> Jaskolski & other experts say in "Stereochemical restraints revisited: how
> accurate are
> refinement targets and
> how much should protein structures be allowed to deviate from them?"
> (2007) Acta Cryst.
> D63:611-620
>
> that
>
> quote: "A correctly set balance will be reflected in root-mean-square
> deviations from ideal
> bond lengths in the
> range 0.015-0.020 A for structures refined to R factors of 0.15-0.20."
>
> I would set the weigth manually.
>
> ~L~
>
> ___
>
>  Lari Lehtiö
>  Structural Genomics Consortium
>  Medical Biochemistry & Biophysics Dept.
>  Karolinska Institute
>  Stockholm, Sweden
> ___
>
> - Original Message -
> From: Mark Mayer <[EMAIL PROTECTED]>
> Date: Tuesday, September 11, 2007 10:08 pm
> Subject: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds
> To: CCP4BB@JISCMAIL.AC.UK
>
>> Hello all,
>>
>> I believer the suggested matrix weight for running refmac is
>> 'auto'. I'm at the end of refinment for
>> a data set that I've cut at 1.59 A, so maps are pretty. Here's the
>> logfile with auto weighting ...
>>
>> NOTE bond rmsds !!!
>>
>> REMARK   3   R VALUE(WORKING SET) :   .15481
>> REMARK   3   FREE R VALUE :   .18739
>> REMARK   3   BOND LENGTHS REFINED ATOMS(A):  4387 ;  .033 ;
>> .022
>> REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  5972 ; 2.776 ;
>> 1.990
>> Am I correct that at this resolution one should aim for bond rmsds
>> of < 0.02. e.g for a weight of
>> 1.0 the rmsd is 0.017, which seems more reasonable.
>>
>> REMARK   3   R VALUE(WORKING SET) :   .16228
>> REMARK   3   FREE R VALUE :   .19032
>> REMARK   3   BOND LENGTHS REFINED ATOMS(A):  4387 ;  .017 ;
>> .022
>> REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  5972 ; 1.689 ;
>> 1.990
>> I know this has been discussed many times before, but expert
>> opinion always appreciated.
>>
>> Thanks - Mark
>>
>

[ccp4bb] High Rfac/Rfree for a 1.6A reso structure

[Santarsiero, Bernard D.]

On Fri, August 17, 2007 10:56 am, Eleanor Dodson wrote:
> There are obvious ones like - incomplete structure etc, but have you
> tried TLS? Sometimes this can  dramaticaly improve the R factors.
>



When people run TLS, are they trying to improve the R-factors, or actually
generate a reasonable model for the structure? I really think people
should be extremely cautious in just turning on the TLS option with dozens
of arbitrary groups during refinement without thinking about the resultant
model.

Bernie Santarsiero

[ccp4bb] The importance of USING our validation tools

[Santarsiero, Bernard D.]

Sorry, I think it's a waste of resources to store the raw images. I think
we should trust people to be able to at least process their own data set.
Besides, you would need to include beamline parameters, beam position,
detector distances, etc. that may or may not be correct in the image
headers. I'm all for storage and retrieval of a primary intensity data
file (I or F^2 with esds).

Bernie Santarsiero


On Thu, August 16, 2007 9:46 am, Mischa Machius wrote:
> Hmm - I think I miscalculated, by a factor of 100 even!... need more
> coffee. In any case, I still think it would be doable. Best - MM
>
>
> On Aug 16, 2007, at 9:30 AM, Mischa Machius wrote:
>
>> I don't think archiving images would be that expensive. For one, I
>> have found that most formats can be compressed quite substantially
>> using simple, standard procedures like bzip2. If optimized, raw
>> images won't take up that much space. Also, initially, only those
>> images that have been used to obtain phases and to refine finally
>> deposited structures could be archived. If the average structure
>> takes up 20GB of space, 5,000 structures would be 1TB, which fits
>> on a single hard drive for less than $400. If the community thinks
>> this is a worthwhile endeavor, money should be available from
>> granting agencies to establish a central repository (e.g., at the
>> RCSB). Imagine what could be done with as little as $50,000. For
>> large detectors, binning could be used, but giving current hard
>> drive prices and future developments, that won't be necessary. Best
>> - MM
>>
>>
>> On Aug 16, 2007, at 9:13 AM, Phil Evans wrote:
>>
>>> What do you count as raw data? Rawest are the images - everything
>>> beyond that is modellling - but archiving images is _expensive_!
>>> Unmerged intensities are probably more manageable
>>>
>>> Phil
>>>
>>>
>>> On  16 Aug 2007, at 15:05, Ashley Buckle wrote:
>>>
 Dear Randy

 These are very valid points, and I'm so glad you've taken the
 important step of initiating this. For now I'd like to respond to
 one of them, as it concerns something I and colleagues in
 Australia are doing:
>
> The more information that is available, the easier it will be to
> detect fabrication (because it is harder to make up more
> information convincingly). For instance, if the diffraction data
> are deposited, we can check for consistency with the known
> properties of real macromolecular crystals, e.g. that they
> contain disordered solvent and not vacuum. As Tassos Perrakis
> has discovered, there are characteristic ways in which the
> standard deviations depend on the intensities and the
> resolution. If unmerged data are deposited, there will probably
> be evidence of radiation damage, weak effects from intrinsic
> anomalous scatterers, etc. Raw images are probably even harder
> to simulate convincingly.

 After the recent Science retractions we realised that its about
 time raw data was made available. So, we have set about creating
 the necessary IT and software to do this for our diffraction
 data, and are encouraging Australian colleagues to do the same.
 We are about a week away from launching a web-accessible
 repository for our recently published (eg deposited in PDB) data,
 and this should coincide with an upcoming publication describing
 a new structure from our labs. The aim is that publication occurs
 simultaneously with release in PDB as well as raw diffraction
 data on our website. We hope to house as much of our data as
 possible, as well as data from other Australian labs, but
 obviously the potential dataset will be huge, so we are trying to
 develop, and make available freely to the community, software
 tools that allow others to easily setup their own repositories.
 After brief discussion with PDB the plan is that PDB include
 links from coordinates/SF's to the raw data using a simple handle
 that can be incorporated into a URL.  We would hope that we can
 convince the journals that raw data must be made available at the
 time of publication, in the same way as coordinates and structure
 factors.  Of course, we realise that there will be many hurdles
 along the way but we are convinced that simply making the raw
 data available ASAP is a 'good thing'.

 We are happy to share more details of our IT plans with the
 CCP4BB, such that they can be improved, and look forward to
 hearing feedback

 cheers
>>
>>
>> --
>> --
>> Mischa Machius, PhD
>> Associate Professor
>> UT Southwestern Medical Center at Dallas
>> 5323 Harry Hines Blvd.; ND10.214A
>> Dallas, TX 75390-8816; U.S.A.
>> Tel: +1 214 645 6381
>> Fax: +1 214 645 6353
>
>
> 
> 
> Mischa Machius, PhD
> Associate Profes

[ccp4bb] PDB format survey?

[Santarsiero, Bernard D.]

Can I ask a dumb question? Just curious...

Why are we now limited to 80 "columns"? In the old days, that was a limit
with Fortran and punched cards. Can a "record" (whatever it's called now)
be as long as we wish? Instead of compressing a lot on a PDB record line,
can we lengthen it to 130 columns?


Bernie Santarsiero


On Fri, August 10, 2007 10:10 am, Warren DeLano wrote:
> Correction:  Scratch what I wrote -- the PDB format does now support a
> formal charge field in columns 79-80 (1+,2+,1- etc.).  Hooray!
>
> Thus, adoption of the CONECT valency convention is all it would take for
> us to be able to convey chemically-defined structures using the PDB
> format.
>
> I'll happily add two-letter chain IDS and hybrid36 to PyMOL but would
> really, really like to see valences included as well -- widespread
> adoption of that simple convention would represent a major practical
> advance for interoperability in structure-based drug discovery.
>
> Cheers,
> Warren
>
>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
>> Behalf Of Warren DeLano
>> Sent: Thursday, August 09, 2007 5:53 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] PDB format survey?
>>
>> Joe,
>>
>> I feel that atom serial numbers are particularly important,
>> since they, combined with CONECT records, provide the only
>> semi-standard convention I know of for reliably encoding bond
>> valences information into a PDB file.
>>
>> single bond = bond listed once
>> double bond = bond listed twice
>> triple bond = bond listed thrice
>> aromatic bond = bond listed four times.
>>
>> This is a convention long supported by tools like MacroModel
>> and PyMOL.
>> For example, here is formaldehyde, where the bond between
>> atoms 1 and 3 is listed twice:
>>
>> HETATM1  C01 C=O 1   0.000  -0.020   0.000  0.00  0.00
>> C
>> HETATM2  N01 C=O 1   1.268  -0.765   0.000  0.00  0.00
>> N
>> HETATM3  O02 C=O 1   0.000   1.188   0.000  0.00  0.00
>> O
>> HETATM4  H01 C=O 1   1.260  -1.775   0.000  0.00  0.00
>> H
>> HETATM5  H02 C=O 1   2.146  -0.266   0.000  0.00  0.00
>> H
>> HETATM6  H03 C=O 1  -0.946  -0.562   0.000  0.00  0.00
>> H
>> CONECT12
>> CONECT13
>> CONECT13
>> CONECT16
>> CONECT2145
>> CONECT31
>> CONECT31
>> CONECT42
>> CONECT52
>> CONECT61
>>
>> I second the proposal of treating this field as a unique
>> string rather than a numeric quantity.
>>
>> Two letter chain IDs would be fine with me, but I do think we
>> could also make better use of SEGI and/or MODEL to break
>> things up while still preserving the utility of certain other
>> records (SHEET, HELIX, etc.) within their existing column definitions.
>>
>> However, we are still lacking a standard way of designating
>> formal charges, So maybe that free column could be better
>> used for encoding a formal charge, such as ["q" "t", "d",
>> "-", "+", "D", "T", "Q"] over the formal charge range of
>> [-4,-3,-2,-1,0,1,2,3,4] -- just an idea :)...
>>
>> With valences plus formal charges along with expansion of the
>> cap on atom counts, I think we could support
>> chemically-complete PDB files and push back the date of PDB
>> demise for a few more years!
>>
>> A Wiki dedicated to practical PDB file hacks and extensions
>> is a superb idea -- of course, the goal should be to
>> ultimately come up with a single well-defined standard set of
>> hacks we all agree upon by supporting them in our code.
>>
>> Cheers,
>> Warren
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
>> Behalf Of Joe Krahn
>> Sent: Thursday, August 09, 2007 1:15 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] PDB format survey?
>>
>> Edward A. Berry wrote:
>> > Ethan A Merritt wrote:
>> >> On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote:
>> >>> Implementations to generate intuitive, maximally backward
>> compatible
>> >>> numbers can be found here:
>> >>>
>> >>>   http://cci.lbl.gov/hybrid_36/
>> >>
>> >> From that URL:
>> >>
>> >> ATOM  8  SD  MET L  48.231 -64.383  -9.257  1.00
>> >> 11.54   S
>> >> ATOM  9  CE  MET L  49.398 -63.242 -10.211  1.00
>> >> 14.60   C
>> >> ATOM  A  N   VAL LA000  52.228 -67.689 -12.196  1.00
>> >> 8.76   N
>> >> ATOM  A0001  CA  VAL LA000  53.657 -67.774 -12.458  1.00
>> >> 3.40   C
>> >>
>> >> Could you please clarify this example?
>> >> Is that "A" a hexidecimal number, or is it a decimal
>> number that
>> >> just happens to have an "A" in front of it?
>> >> [A-Z][0-] gives a larger range of values than 5 bytes of
>> hexadecimal,
>> >> so I'm guessing it's the former.  But the example is not clear.
>> >>
>> > I'm guessing the former also. A 5-digit hex number would not be
>> > backwards compatible. With this system legacy programs can
>> still read
>> > 

Re: [ccp4bb] Popularity of Stereo graphics in crystallography

[Santarsiero, Bernard D.]

I agree with Kevin. We have stereo on about half of our workstations, and
no one has used them in about three years. We typically use "O".

Also, we have three large servers which are relatively fast. So the main
purpose of a workstation is building, not computing here. That way you can
easily work on multiple structures on a workstation at the same time,
while you're refining and building them. We have a few people that use
PC's and Coot as well.

Bernie


On Wed, June 20, 2007 11:45 am, P Hubbard wrote:
> Hi,
>
> Thanks for the e-mail. The current results of the survey would certainly
> put
> you in the minority! Stereo graphics are not dead after all.
>
> I have used systems with and without stereo graphics. I personally prefer
> them, and think they are great for helping newbies refine, and for
> non-structural biologists and students to look at molecular architecture.
> It
> seems a lot of other people, for whatever reason, like them too.
>
> Paul
>
>
>>From: Kevin Cowtan <[EMAIL PROTECTED]>
>>Reply-To: Kevin Cowtan <[EMAIL PROTECTED]>
>>To: CCP4BB@JISCMAIL.AC.UK
>>Subject: Re: [ccp4bb] Survey on computer usage in crystallography
>>Date: Wed, 20 Jun 2007 17:27:04 +0100
>>
>>More likely the issue is that some of us do not find stereo to be
>> necessary
>>of beneficial for crystallographic model building.
>>
>>In which case, given the power of modern PCs and graphics cards, a basic
>>off-the-shelf PC costing $1000/£500 is completely adaquate for typical
>>structure solution and model building problems.
>>
>>I use coot a lot and I haven't even bothered installing the graphics
>>drivers for my graphics card. All the 3D stuff gets gone in software, and
>>most of the graphics hardware sits around doing nothing. If I needed the
>>performance, it would be a 5 minute job to install the drivers, but I
>>haven't needed it.
>>
>>Kevin
>>
>>P Hubbard wrote:
>>>I am sorry you are unhappy with the questions, David.
>>>
>>>As I am sure you know, I half-decent system with stereo graphics doesn't
>>>come cheap, and if you price things together to make something that
>>>performs well I doubt you'll get much change out of $2000.
>>>
>>>I am aware of other 3D systems (such as those listed on
>>> www.stereo3d.com).
>>>However, the price of peripherals like a 3D LCD monitor are
>>> prohibitively
>>>expensive (and the quality of the images is supposed to be poor). Do you
>>>know of a relatively inexpensive way of displaying 3D images on PCs?
>>>
>>>Any other comments would be greatly appreciated.
>>>
>>>Paul
>
> _
> Get a preview of Live Earth, the hottest event this summer - only on MSN
> http://liveearth.msn.com?source=msntaglineliveearthhm
>

Re: [ccp4bb] Highest shell standards

[Santarsiero, Bernard D.]

I seem to recall this being discussed at some point.

For the difference electron density map, there clearly isn't a downside to
loss of reflections, i.e., the coefficients in the map generation are
formally zero for Fo-Fc (which all the scaling, weight, sigma-A bits in
there). If the phases are fairly good, then you are assuming that the Fobs
agrees perfectly with the Fcalc. You don't gain any new details in the
map, but the map isn't distorted with loss of these terms.

As for the 2Fo-Fc (2mFo-DFc, or something like that) electron density map,
it again assumes that the phases are in good shape, and you essentially
lose any new information you could gain from the addition of new Fobs
terms, but the map isn't distorted since the terms are zero.

I seem to recall in the dark ages that you could make an Fobs map, and
included Fcalc, or some fraction of Fcalc (like 0.5Fc) in as the Fobs term
for missing reflections. That way the amplitudes are closer to being
correct for resolution shells that are fairly incomplete. Anyone else
remember this for small molecule structures?

The real issue, generally, is that the phases are the most important
factor in making a good map, and the structure factors are, unfortunately,
weaker contributors to features in the maps.

Bernie




On Fri, March 23, 2007 4:02 am, Eleanor Dodson wrote:
> This is a good point - I had thought that D would be very low for an
> incomplete shell, but that doesnt seem to be true..
>
> Garib - what do you think?
> Eleanor
>
>
> Petrus H Zwart wrote:
>>> I typically process my data to a maximum I/sig near 1, and
>>> completeness in
>>> the highest resolution shell to 50% or greater. It
>>>
>>
>> What about maps computed of very incomplete datasets at high resolution?
>> Don't you get a false sense of details when the missing reflections are
>> filled in with DFc when computing a 2MFo-DFc map?
>>
>> P
>>
>>
>>
>

Re: [ccp4bb] X-ray generator uninterruptible power supply

[Santarsiero, Bernard D.]

On Thu, March 22, 2007 3:46 pm, William Scott wrote:
> Hi Citizens:
>
> Does anyone use an uninterruptible power supply for their X-ray
> generator?  Here at UCDIY, the electricity supply is pretty sketchy,
> and it is hammering our X-ray generator every time someone forgets to
> feed the hamster or grease his wheel. If so, how much does such a
> thing cost, and how unpleasant is it to maintain (since at UCDIY, you
> get to do all your own maintenance)?
>
> Thanks in advance.
>
> Bill
>
You may want to consider power conditioners in the line rather than actual
uninterruptible power supply systems. I think Ray Stevens at Scripps has
uninterruptible power on his generator, so give him a call.

Bernie

Re: [ccp4bb] Highest shell standards

[Santarsiero, Bernard D.]

My guess is that the integration is roughly the same, unless the profiles
are really poorly defined, but that the scaling that is suffering from
using a lot of high-resolution weak data. We've integrated data to say
I/sig = 0.5, and sometimes seem more problems with scaling. I then cut
back to I/sig = 1 and it's fine. The major difficulty arises that if the
crystal is dying, and the decay/scaling/absorption model isn't good
enough. So that's definately a consideration when trying to get a more
complete data set and higher resolution (so more redundancy).

Bernie


On Thu, March 22, 2007 12:21 pm, Jose Antonio Cuesta-Seijo wrote:
> I have observed something similar myself using Saint in a Bruker
> Smart6K detector and using denzo in lab and syncrotron detectors.
> First the I over sigma never really drops to zero, no mater how much
> over your real resolution limit you integrate.
> Second, if I integrate to the visual resolution limit of, say, 1.5A,
> I get nice dataset statistics. If I now re-integrate (and re-scale)
> to 1.2A, thus including mostly empty (background) pixels everywhere,
> then cut the dataset after scaling to the same 1.5A limit, the
> statistics are much worse, booth in I over sigma and Rint. (Sorry, no
> numbers here, I tried this sometime ago).
> I guess the integration is suffering at profile fitting level while
> the scaling suffers from general noise (those weak reflections
> between 1.5A and 1.2A will be half of your total data!).
> I would be careful to go much over the visual resolution limit.
> Jose.
>
> **
> Jose Antonio Cuesta-Seijo
> Cancer Genomics and Proteomics
> Ontario Cancer Institute, UHN
> MaRs TMDT Room 4-902M
> 101 College Street
> M5G 1L7 Toronto, On, Canada
> Phone:  (416)581-7544
> Fax: (416)581-7562
> email: [EMAIL PROTECTED]
> **
>
>
> On Mar 22, 2007, at 10:59 AM, Sue Roberts wrote:
>
>> I have a question about how the experimental sigmas are affected
>> when one includes resolution shells containing mostly unobserved
>> reflections.  Does this vary with the data reduction software being
>> used?
>>
>> One thing I've noticed when scaling data (this with d*trek (Crystal
>> Clear) since it's the program I use most) is that I/sigma(I) of
>> reflections can change significantly when one changes the high
>> resolution cutoff.
>>
>> If I set the detector so that the edge is about where I stop seeing
>> reflections and integrate to the corner of the detector, I'll get a
>> dataset where I/sigma(I) is really compressed - there is a lot of
>> high resolution data with I/sigma(I) about 1, but for the lowest
>> resolution shell, the overall I/sigma(I) will be maybe 8-9.  If the
>> data set is cutoff at a lower resolution (where I/sigma(I) in the
>> shell is about 2) and scaled, I/sigma(I) in the lowest resolution
>> shell will be maybe 20 or even higher (OK, there is a different
>> resolution cutoff for this shell, but if I look at individual
>> reflections, the trend holds).  Since the maximum likelihood
>> refinements use sigmas for weighting this must affect the
>> refinement.  My experience is that interpretation of the maps is
>> easier when the cut-off datasets are used. (Refinement is via
>> refmac5 or shelx).  Also, I'm mostly talking about datasets from
>> well-diffracting crystals (better than 2 A).
>>
>> Sue
>>
>>
>> On Mar 22, 2007, at 2:29 AM, Eleanor Dodson wrote:
>>
>>> I feel that is rather severe for ML refinement - sometimes for
>>> instance it helps to use all the data from the images, integrating
>>> right into the corners, thus getting a very incomplete set for the
>>> highest resolution shell.  But for exptl phasing it does not help
>>> to have many many weak reflections..
>>>
>>> Is there any way of testing this though? Only way I can think of
>>> to refine against a poorer set with varying protocols, then
>>> improve crystals/data and see which protocol for the poorer data
>>> gave the best agreement for the model comparison?
>>>
>>> And even that is not decisive - presumably the data would have
>>> come from different crystals with maybe small diffs between the
>>> models..
>>> Eleanor
>>>
>>>
>>>
>>> Shane Atwell wrote:

 Could someone point me to some standards for data quality,
 especially for publishing structures? I'm wondering in particular
 about highest shell completeness, multiplicity, sigma and Rmerge.

 A co-worker pointed me to a '97 article by Kleywegt and Jones:

 _http://xray.bmc.uu.se/gerard/gmrp/gmrp.html_

 "To decide at which shell to cut off the resolution, we nowadays
 tend to use the following criteria for the highest shell:
 completeness > 80 %, multiplicity > 2, more than 60 % of the
 reflections with I > 3 sigma(I), and Rmerge < 40 %. In our
 opinion, it is better to have a good 1.8 Å structure, than a poor
 1.637 Å structure."

 Are these recommendations still valid with maximum likel

Re: [ccp4bb] Highest shell standards

[Santarsiero, Bernard D.]

There are journals that have specific specifications for these parameters,
so it matters where you publish. I've seen restrictions that the highest
resolution shell has to have I/sig > 2 and completeness > 90%. Your
mileage may vary.

I typically process my data to a maximum I/sig near 1, and completeness in
the highest resolution shell to 50% or greater. It's reasonable to expect
the multiplicity/redundancy to be greater than 2, though that is difficult
with the lower symmetry space groups in triclinc and monoclinic systems
(depending upon crystal orientation and detector geometry). The chi^2's
should be relatively uniform over the entire resolution range, near 1 in
the highest resolution bins, and near 1 overall. With this set of
criteria, R(merge)/R(sym) (on I) can be as high as 20% and near 100% for
the highest resolution shell. R is a poor descriptor when you have a
substantial number of weak intensities because it is dominated by the
denominator; chi^2's are a better descriptor since it has, essentially,
the same numerator.

One should also note that the I/sig criteria can be misleading. It is the
*average* of the I/sig in a resolution shell, and as such, will include
intensities that are both weaker and stronger than the average. For the
highest resolution shell, if you discard intensities greater than 2sig,
then you are also discarding intensities substantially greater than 2sig
as well. The natural falloff of the intensities is reflected (no pun
intended) by the average B-factor of the structure, and you need the
higher resolution, weaker data to best define that parameter.

Protein diffraction data is inherently weak, and far weaker than we obtain
for small molecule crystals. Generally, we need all the data we can get,
and the dynamic range of the data that we do get is smaller than that
observed for small molecule crystals. That's why we use restraints in
refinement. An observation of a weak intensity is just as valid as the
observation of a strong observation, since you are minimizing a function
related to matching Iobs to Icalc. This is even more valid with refinement
targets like the maximum likelihood function. The ONLY reasons that we
ever used I/sig or F/sig cutoffs in refinements was to make the
calculations faster (since we were substantially limited by computing
power decades ago), the sig's were not well-defined for weak intensities
(especially for F's), and the detectors were not as sensitive. Now, with
high brilliance x-ray sources and modern detectors, you can, in fact,
measure weak intensities well--far better than we could decades ago. And
while the dynamic range of intensities for a protein set is relatively
flat, in comparison to a small molecule dataset, those weak terms near
zero are important in restraining the Fcalc's to be small, and therefore
helping to define the phases properly.

In 2007, I don't see a valid argument of severe cutoff's in I/sig at the
processing stage. I/sig = 1 and a reasonable completeness of 30-50% in the
highest resolution shell should be adequate to include most of the useful
data. Later on, during refinement, you can, indeed, increase the
resolution limit, if you wish. Again, with targets like maximum
likelihood, there is no statistical reason to do that. You do it because
it makes the R(cryst), R(free), and FOM look better. You do it because you
want to have a 2.00A vs. 1.96A resolution structure. What is always true
is that you need to look at the maps, and they need as many terms in the
Fourier summation as you can include. There should never be an argument
that you're savings on computing cycles. It's takes far longer to look
carefully at an electron density map and make decisions on what to do than
to carry out refinement. We're rarely talking about twice the computing
time, we're probably thinking 10% more. That's definately not a reason to
throw out data. We've got lots of computing power and lots of disk
storage, let's use to our advantage.

That's my nickel.

Bernie Santarsiero




On Thu, March 22, 2007 7:00 am, Ranvir Singh wrote:
> I will agree with Ulrich. Even at 3.0 A, it is
> possible to have a  structure with reasonable accuracy
> which can explain the biological function/ or is
> consistent with available biochemical data.
> Ranvir
> --- Ulrich Genick <[EMAIL PROTECTED]> wrote:
>
>> Here are my 2-3 cents worth on the topic:
>>
>> The first thing to keep in mind is that the goal of
>> a structure
>> determination
>> is not to get the best stats or to claim the highest
>> possible
>> resolution.
>> The goal is to get the best possible structure and
>> to be confident that
>> observed features in a structure are real and not
>> the result of noise.
>>
>>  From that perspective, if any of the conclusions
>> one draws from a
>> structure
>> change depending on whether one includes data with
>> an I/sigI in the
>> highest
>> resolution shell of 2 or 1, one probably treads on
>> thin ice.
>>
>> The general guide that one should include o

Re: [ccp4bb] Data collection of SAD (MAD) data of Copper-containing protein

[Santarsiero, Bernard D.]

It would be useful to know how you tried to solve the structure by MR.
Just because there is a large number of chains in the ASU isn't a reason
that MR will fail. At times you need to find some of the chains, do some
rebuilding, and then use that amended model for a continued search.

Bernie Santarsiero
Univ of Illinois at Chicago


On Thu, March 15, 2007 12:00 pm, Yi Xue wrote:
> Dear all:
>   We already got nice crystals of a drug-protein complex, however, MR
> failed due to the huge copies (>12) of protein molecules per asu. Protein
> itself is a small one, only ~70 aa.
>  Later on, we collected MAD data of copper (copper : protein ~ 1: 1),
> Rsym of the data was around ~9%,  the anomalous signals were weak, and
> only
> good to ~6A,  the data also failed to solve the phases.
>  Thus, basically, the Cu anomallous signal is very weak, and the
> crystals are kind of sensitive to radiation, it is dying but not that
> fast.
>  I am wondering,  Do we stand any chances to solve the phases by Cu
> MAD
> or SAD?
>
>
> Any suggestions or comments are highly appreciated?
> Yi
>

Re: [ccp4bb] Differences in R and Rfree

[Santarsiero, Bernard D.]

I'm sure that the relative weight between your structure factors and
geometric factors is wrong. If you use the default value, 0.3, it may or
may not be too high. In CNS, the relative weight factor is calculated, but
this is not done in REFMAC. As a rough rule-of-thumb, I aim for a rmsd of
bond lengths at 0.01A and rmsd of bond angles at 1.5deg. This works
reasonably well for both CNS and REFMAC. I think you'll find that your
rmsd is quite high for the REFMAC coordinates since you've relaxed the
geometric factors too much to match the structure factor differences.

Bernie Santarsiero


On Fri, March 9, 2007 8:22 pm, Nicholas Noinaj wrote:
> Hi,
>
> I am working on a 2.4 angstrom structure that is in its final stages of
> refinement and finding that REFMAC5 is giving a large difference between R
> and Rfree (10%), 0.16 and 0.29, respectively.  2Fo-Fc maps looks great and
> there is very little density in the difference maps.  My model covers the
> entire protein sequence, except for ~5 residues on N-term and 3 residues
> on C-term.  I then used the model for refinement (annealing) within CNS,
> and found that R and Rfree are relatively similar, 0.2 and 0.28, but in
> better agreement.
>
> I have read other posts addressing similar questions, but still unsure
> what my problem could be, if there is one.  While I don't mind repeating
> things in CNS, I would really like to learn to be completely reliable on
> CCP4 Suite as much as possible, since i really like the REFMAC5 - Coot
> duo.  I would appreciate any suggestions or comments you might offer.
> Given how nice the density maps look and that the model passes procheck
> analysis with very few suggestions for further investigations, i am unsure
> when to go from here.
>
> Thanks in advance for all feedback!
>
>
>
>
> Cheers,
> Nick
>

Re: [ccp4bb] XDS to MTZ for SOLVE

[Santarsiero, Bernard D.]

OK, thanks to everyone.

The MTZ file can be used, but without the IMEAN and SIGIMEAN entries
included. I could have tried that too.

The SHELX unmerged file option works as well.

Thanks again.

Bernie



On Wed, March 7, 2007 9:58 am, Eleanor Dodson wrote:
> But SOLVE will read an mtz file?
>
> I dont think you need to do this..
> Eleanor
>
> Santarsiero, Bernard D. wrote:
>> Not purely a ccp4 question, but an MTZ file is involved, so stick with
>> me.
>>
>> I've collected a SAD data set, and processed with XDS. I can use XDSCONV
>> to generate an MTZ, SHELX, and CNS file. I chose the MTZ file since it
>> keeps the intensities. SHELX does too (the F**2), but has separate lines
>> for (h,k,l) and (-h,-k,-l). The MTZ file has hkl,IMEAN, SIGIMEAN, I+,
>> SIGI+, I-, SIGI-.
>>
>> I used mtzdump (or could use MTZVARIOUS) to convert this file to a
>> simple
>> ASCII file, and then extracted just the hkl, I+, SIGI+, I-, SIGI-. Since
>> CCP4 fills in all of the reflections in an ASU, I removed those
>> reflection
>> entries with SIGIMEAN = -999.0.
>>
>> I have a file with has some entries with -999 (for the non-measured
>> value), especially those in the centric zones.
>>
>> For SOLVE, does it identify entries with a value of -999 as a
>> placeholder,
>> or should I entirely removed those from the data file? I used the
>> options
>>
>> PREMERGED
>> READFORMATTED
>> READ_INTENSITIES
>>
>> in SOLVE. What if I measured I- but I+? That's why I left them all in.
>>
>> Suggestions on what is best for the solve run? I'm concerned that it's
>> interpretting the -999 as a real measurement.
>>
>> Bernie Santarsiero
>>
>>
>>
>

[ccp4bb] XDS to MTZ for SOLVE

[Santarsiero, Bernard D.]

Not purely a ccp4 question, but an MTZ file is involved, so stick with me.

I've collected a SAD data set, and processed with XDS. I can use XDSCONV
to generate an MTZ, SHELX, and CNS file. I chose the MTZ file since it
keeps the intensities. SHELX does too (the F**2), but has separate lines
for (h,k,l) and (-h,-k,-l). The MTZ file has hkl,IMEAN, SIGIMEAN, I+,
SIGI+, I-, SIGI-.

I used mtzdump (or could use MTZVARIOUS) to convert this file to a simple
ASCII file, and then extracted just the hkl, I+, SIGI+, I-, SIGI-. Since
CCP4 fills in all of the reflections in an ASU, I removed those reflection
entries with SIGIMEAN = -999.0.

I have a file with has some entries with -999 (for the non-measured
value), especially those in the centric zones.

For SOLVE, does it identify entries with a value of -999 as a placeholder,
or should I entirely removed those from the data file? I used the options

PREMERGED
READFORMATTED
READ_INTENSITIES

in SOLVE. What if I measured I- but I+? That's why I left them all in.

Suggestions on what is best for the solve run? I'm concerned that it's
interpretting the -999 as a real measurement.

Bernie Santarsiero

Re: [ccp4bb] practical limits of MR?

[Santarsiero, Bernard D.]

On Mon, March 5, 2007 2:16 pm, Nat Echols wrote:
> I had a debate with a coworker about using MR in desperation and I'm
> curious what the most extreme case is where a very different model was
> used to solve a structure.  This could be highest RMSD, lowest % identity,
> or most incomplete model.  I'm also curious whether homology modelling has
> ever been useful for this.  (I'm pretty sure I've come across papers
> discussing this last concept.)
>
> thanks,
> Nat
>

I'm not sure what "in desperation" means. You're trying to solve a
structure, so all options are open, right? They don't have to be elegant,
it just has to work. :)

I know of a few cases where roughly 15% of a structure was used as a
search model to solve a structure. Recently I used about 30% of the
structure to get the initial model with MR, and then bootstrap along to
find the remainder. Similarly, you can get away with 25-30% sequence
homology (so long as there is high structural homology) with MR. It's
relatively easy to find a helix-turn-helix motif by MR than, say, an
extended beta-sheet expanse, because the beta-sheet can substantially bend
and twist, whereas the helices are fairly rigid.

Bernie Santarsiero

[ccp4bb] [Fwd: Re: [ccp4bb] how many stuck datasets are actually twinned?]

[Santarsiero, Bernard D.]

-

It's very possible with any overlap of lattice points, even in the lower
symmetry space groups. To extend Eleanor's list: For example, I once had a
structure with the unit cell relationship 3c cos(beta) = -a. In cases like
that, it's not really a clean diffraction, but looks very much like a
single lattice of points. This is so-called "reticular pseudomerohedry
across the ab-plane with a twin index of 3." The h,k,l reflections of the
parent lattice are superimposed upon h, k, (-l-2h)/3 reflections of the
twin lattice. So twinning can be frightenly common.

On Wed, February 21, 2007 10:49 am, Eleanor Dodson wrote:
> There are many and various reasons for unpleasantly high R values,  and
> twinning is undoubtedly one of them.
>
> But you can only have twinning with apparently good diffraction if the
> cell dimensions allow it.
>
> It is always a possibility in trigonal, tetragonal and cubic cells.
>
> Certain other combinations of cell dimensions allow it ;- eg monoclinic
> with a ~= c   or beta ~= 90
>
> But you can usually detect it from the intensity statistics - see the
> plots from TRUNCATE for Moments and Cumulative intensities.
>
> Or the output of SFCHECK which suggests possible twinning baed on
> interpretation of  these tests.
>
> So it should be relatively easy to spot those cases where twinning is a
> likely cause of high Rfactor..
>
> Surprisingly some degree of twinning doesnt seem to degrade the map
> quality very much..
>
> Just an aside - it is really puzzling why from two sets of apparently
> similar data, one set gives Rfacros of 24+ while others  refine to R of
> 18% ..
> Eleanor
>
>
>
>
> Kay Diederichs wrote:
>> Sue Roberts wrote:
>>> Hello
>>>
>>> A partially philosophical, partially pragmatic question.
>>>
>>> I've noticed a trend, both on ccp4bb and locally, to jump to twinning
>>> as an explanation for data sets which do not refine well - that is
>>> data sets with R and Rfree stuck above whatever the person's
>>> pre-conceived idea of an acceptable R and Rfree are.   This usually
>>> leads to a mad chase through all possible space groups, twinning
>>> refinements, etc. and, in my experience, often results in a lot of
>>> time being spent for no significant improvements.
>>>
>>> Just out of curiosity, does  anyone have a feel for what fraction of
>>> stuck data sets are actually twinned? (I presume this will vary
>>> somewhat with the type of problem being worked on).
>>>
>>> And a  sorta-hypothetical question, given nice-looking crystals;
>>> images with no visible split spots, extra reflections, or streaks;
>>> good predictions; nice integration profiles; good scaling with
>>> reasonable systematic absences; a normal solvent content; and a
>>> plausible structure solution,  and R/Rf somewhat highish (lets say
>>> .25/.3  for 1.8 A data), how often would you expect the Stuck R/Rf to
>>> be caused by twinning (or would you not consider this a failed
>>> refinement).  (My bias is that such data sets are almost never
>>> twinned and one should look elsewhere for the problem, but perhaps
>>> others know better.)
>>>
>>> Sue
>>> Sue Roberts
>>> Biochemistry & Biopphysics
>>> University of Arizona
>>>
>>> [EMAIL PROTECTED]
>>
>> Sue,
>>
>> I seem to be in the other camp:  - "nice-looking crystals; images
>> with no visible split spots, extra reflections, or streaks; good
>> predictions; nice integration profiles; good scaling with reasonable
>> systematic absences; a normal solvent content; and a plausible structure
>> solution,  and R/Rf somewhat highish (lets say .25/.3  for 1.8 A data)"
>>
>> - all of this may happen with merohedrally twinned crystals. I believe
>> it would be good to teach students to always devote some thought to
>> the possibility of merohedral twinning in case of a trigonal/
>> hexagonal/ tetragonal crystal, to avoid a rather common pitfall. I
>> don't have the percentage at hand, but I believe I saw a paper by
>> George Sheldrick giving a high percentage (like 20% or so) of
>> merohedral twinned structures in the above crystal systems for
>> small-molecule structures -  why should that percentage be different
>> for protein crystals?
>>
>> It is of course true that twinning refinement is painful, and a lot of
>> additional work! But "man twinning" is always enlightening reading.
>>
>> Kay
>

Re: [ccp4bb] how many stuck datasets are actually twinned?

[Santarsiero, Bernard D.]

It's very possible with any overlap of lattice points, even in the lower
symmetry space groups. To extend Eleanor's list: For example, I once had a
structure with the unit cell relationship 3c cos(beta) = -a. In cases like
that, it's not really a clean diffraction, but looks very much like a
single lattice of points. This is so-called "reticular pseudomerohedry
across the ab-plane with a twin index of 3." The h,k,l reflections of the
parent lattice are superimposed upon h, k, (-l-2h)/3 reflections of the
twin lattice. So twinning can be frightenly common.

On Wed, February 21, 2007 10:49 am, Eleanor Dodson wrote:
> There are many and various reasons for unpleasantly high R values,  and
> twinning is undoubtedly one of them.
>
> But you can only have twinning with apparently good diffraction if the
> cell dimensions allow it.
>
> It is always a possibility in trigonal, tetragonal and cubic cells.
>
> Certain other combinations of cell dimensions allow it ;- eg monoclinic
> with a ~= c   or beta ~= 90
>
> But you can usually detect it from the intensity statistics - see the
> plots from TRUNCATE for Moments and Cumulative intensities.
>
> Or the output of SFCHECK which suggests possible twinning baed on
> interpretation of  these tests.
>
> So it should be relatively easy to spot those cases where twinning is a
> likely cause of high Rfactor..
>
> Surprisingly some degree of twinning doesnt seem to degrade the map
> quality very much..
>
> Just an aside - it is really puzzling why from two sets of apparently
> similar data, one set gives Rfacros of 24+ while others  refine to R of
> 18% ..
> Eleanor
>
>
>
>
> Kay Diederichs wrote:
>> Sue Roberts wrote:
>>> Hello
>>>
>>> A partially philosophical, partially pragmatic question.
>>>
>>> I've noticed a trend, both on ccp4bb and locally, to jump to twinning
>>> as an explanation for data sets which do not refine well - that is
>>> data sets with R and Rfree stuck above whatever the person's
>>> pre-conceived idea of an acceptable R and Rfree are.   This usually
>>> leads to a mad chase through all possible space groups, twinning
>>> refinements, etc. and, in my experience, often results in a lot of
>>> time being spent for no significant improvements.
>>>
>>> Just out of curiosity, does  anyone have a feel for what fraction of
>>> stuck data sets are actually twinned? (I presume this will vary
>>> somewhat with the type of problem being worked on).
>>>
>>> And a  sorta-hypothetical question, given nice-looking crystals;
>>> images with no visible split spots, extra reflections, or streaks;
>>> good predictions; nice integration profiles; good scaling with
>>> reasonable systematic absences; a normal solvent content; and a
>>> plausible structure solution,  and R/Rf somewhat highish (lets say
>>> .25/.3  for 1.8 A data), how often would you expect the Stuck R/Rf to
>>> be caused by twinning (or would you not consider this a failed
>>> refinement).  (My bias is that such data sets are almost never
>>> twinned and one should look elsewhere for the problem, but perhaps
>>> others know better.)
>>>
>>> Sue
>>> Sue Roberts
>>> Biochemistry & Biopphysics
>>> University of Arizona
>>>
>>> [EMAIL PROTECTED]
>>
>> Sue,
>>
>> I seem to be in the other camp:  - "nice-looking crystals; images
>> with no visible split spots, extra reflections, or streaks; good
>> predictions; nice integration profiles; good scaling with reasonable
>> systematic absences; a normal solvent content; and a plausible structure
>> solution,  and R/Rf somewhat highish (lets say .25/.3  for 1.8 A data)"
>>
>> - all of this may happen with merohedrally twinned crystals. I believe
>> it would be good to teach students to always devote some thought to
>> the possibility of merohedral twinning in case of a trigonal/
>> hexagonal/ tetragonal crystal, to avoid a rather common pitfall. I
>> don't have the percentage at hand, but I believe I saw a paper by
>> George Sheldrick giving a high percentage (like 20% or so) of
>> merohedral twinned structures in the above crystal systems for
>> small-molecule structures -  why should that percentage be different
>> for protein crystals?
>>
>> It is of course true that twinning refinement is painful, and a lot of
>> additional work! But "man twinning" is always enlightening reading.
>>
>> Kay
>

Re: [ccp4bb] REFMAC5 and Shannon factor

[Santarsiero, Bernard D.]

You didn't say anything about the "weighting term" between the F's and
geometrical parameters. That will substantially affect the R's, and the
default value of 0.3 in REFMAC isn't appropriate for all structures. In
CNS, it's adjusted to a more reasonable value during refinement.

Bernie Santarsiero


On Wed, February 14, 2007 10:36 am, Billy Poon wrote:
> Dear all,
>
> I have been using REFMAC5 to calculate the R values of several structures
> from
> the PDB and was confused by the behavior of the SHANnon_factor keyword.
> When I
> leave it at the default (set at 1.5 in the source code), I get one set of
> R
> values.  But when I manually set the value to 1.5 (SHANnon_factor 1.5) in
> the
> script, I get a different set of values.  Usually, it's off at the third
> or
> fourth decimal place, but for one case (PDB code 2OAU), I get a difference
> of
> about 0.0116 (0.28416 for default, 0.27258 for manual setting) for the R
> value
> and 0.0184 (0.31653 for default, 0.29818 for manual setting) in the Free
> R.
>
> I have tested this on the following architectures and they all behave the
> same
> way:
>
> Intel Xeon (32-bit Linux, REFMAC 5.2.0019, compiled with Intel compilers
> 9.1)
> Intel Itanium2 (64-bit Linux, REFMAC 5.2.0019, compiled with Intel
> compilers
> 9.1)
> AMD Opteron (64-bit Linux, REFMAC 5.2.0019, compiled with GNU compilers
> 3.3.3)
> SGI MIPS (IRIX 6.5, REFMAC 5.2.0003, pre-compiled binaries)
>
> I am not doing any refining of the structures.  I just wanted to see what
> the R
> values are when calculated with REFMAC5 (the structures I was looking at
> were
> refined in CNS or X-PLOR) and was confused by the different results with
> the same setting.  Also, should changing the SHANnon_factor affect the R
> values much?  Thanks in advance for your help!
>
> -Billy
>
> And the script I use is pasted below:
>
> #
> # Refmac
> #
> refmac:
> refmac5 \
> HKLIN ./fo.mtz \
> XYZIN ./2oau.pdb \
> XYZOUT ./test.pdb \
> << eor
> #
> # Do not add hydrogens
> #
> MAKE HYDR N
> MAKE LINK N
> MAKE CHECK NONE
> #
> # Input mtz labels
> #
> LABIN FP=FP SIGFP=SIGFP FREE=FREE
> #
> # Set resolution
> #
> REFI RESOlution 3.7 50.00
> #
> # Define NCS
> #
> NCSR NCHAI 7 CHAI A B C D E F G NSPANS 1 1 254 4
> #
> # Refine overall B factor
> #
> REFI BREF OVERall
> #
> # Set Free flag
> #
> FREE 0
> #
> # Number of refinement cycles
> #
> NCYC 0
> #
> # Monitoring level
> #
> MONI MEDI
> #
> # Change Shannon sampling (commented out if testing default behavior)
> #
> SHANNON_FACTOR 1.5
> #
> # end
> #
> end
> eor
>
>

Re: [ccp4bb] Multi-copies in one assymetric unit

[Santarsiero, Bernard D.]

Assuming that the MR solution is correct (I agree with Eleanor, that you
need to be certain about your selection of space group), then use your
complete model of chain A superimposed on chains B, C, and D. Then refine
and build the heck out of it. In a similar situation, it was relatively
easy for me to find two out of three molecules by MR. We were never really
convinced that there was a third (Matthews coefficient dicey, suggesting
either 2 or 3). After substantial refinement and building, the third chain
was apparent, and we rebuilt it completely. Looking at the average
B-factors of each chain, and the overall packing environment, chain A was
tight, chain B looser, and chain C will substantially fewer contacts.

Bernie Santarsiero


On Tue, February 13, 2007 10:07 am, Eleanor Dodson wrote:
> Sometimes this sort of disorder is due to an error , so the first thing
> is to check very carefully that the solution makes sense.
>
> Why are you so sure there are 6 copies in the asymmetric unit?
>
> In situations like this I first worry about SG.
>
> Is there a pseudo-translation vector? This can make it hard to decide on
> the SG..
>
> Is there an alternate spacegroup with fewer molecules in the asymm unit?
>
> What does the self rotation show?
>
>
>
> Yanming Zhang wrote:
>> Dear All,
>>
>> Maybe this is a trivial question:
>>
>> My data should have 6 molecules in one assymetric unit.  MR could find
>> out 4 molecules. After this, no matter how hard I have tried, no more
>> molecules can be found. At this stage, I suppose that all other copies
>> are dis-ordered. And go ahead to do refinement with 4 molecules (ABCD)
>> available.
>> The density for A is quite good. But for BCD are very dis-ordered.
>> Many breaks in chains. I'd like to ask you:
>> In a situation like this, should I:
>> A, Use NCS for all copies?
>> B Do not use NCS at all?
>> C, Use NCS just for BCD? (even dis-ordered, but similar)?
>> What is the trick to lower down Rfree as soon as possible, if you have
>> experienced the same situation before?
>>
>>
>> Thanks
>>
>> Yanming
>>
>>
>

Re: [ccp4bb] "B" in B-factor

[Santarsiero, Bernard D.]

page 79, chapter 5

On Wed, January 24, 2007 1:43 pm, Diana Tomchick wrote:
> Yes, it is! I somehow missed that when checking the IUCr web site.
> Virtually the whole publication is available as a series of
> downloadable PDF files, though for some strange reason the indices
> are listed but not available. Without the Name Index it would have
> taken a huge amount of time to locate the pertinent sections in a 700
> page book.
>
> Diana
>
> On Jan 24, 2007, at 1:23 PM, Miller, Mitchell D. wrote:
>
>> Hi Diana,
>> Is this the same publication you are referring to?
>> http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/index.html
>>
>> Regards,
>> Mitch
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf
>> Of Diana Tomchick
>> Sent: Wednesday, January 24, 2007 11:09 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] "B" in B-factor
>>
>> An interesting discussion of the development of the Debye-Waller
>> correction can be found in the IUCr publication, "Fifty Years of X-
>> Ray Diffraction," edited by P.P. Ewald (unfortunately, it's no longer
>> in print). It seems that Debye was the first scientist to tackle "a
>> problem which appeared to others hopelessly complicated at the time:
>> the influence of the temperature motion of the atoms on the
>> diffraction of X-rays (p. 79 of aforementioned publication)."
>> Interestingly, his original formulation of the correction included
>> the constant M, "which can be expressed by means of the elastic
>> properties of the crystal or their combination, the 'Debye
>> Temperature', which occurs in the theory of the specific heat (same
>> reference)." The text goes on to mention that Ivar Waller
>> demonstrated in 1923 that Debye's expression for M was wrong by a
>> factor of two. No mention is given in "Fifty Years" of a "B factor"
>> but it sounds as though Waller decided to use a different
>> nomenclature in his paper from 1927 to avoid confusion.
>>
>> Too bad that "Fifty Years" is no longer in print, though used copies
>> can be purchased from various on-line booksellers. It provides a very
>> enlightening and easily readable history of the early days in the
>> field, and the interchange of scientists and ideas across the
>> Atlantic Ocean.
>>
>> Diana
>>
>>
>> On Jan 24, 2007, at 11:14 AM, Santarsiero, Bernard D. wrote:
>>
>>> It looks like the earliest reference to the Debye-Waller factor is
>>> from
>>> Debye's paper:
>>>
>>> Uber den Einfluss der Warmebewegung uf die Interferenzerscheinungen
>>> beiu
>>> Rontgenstrahlen, Verhandl. deut. phyik. Ges., 15, 678-689 (1913),
>>>
>>> and the succeeding paper Verhandl. deut. phyik, Ges., 15, 738-752
>>> (1913),
>>>
>>> and Waller:
>>>
>>> Die Einwirkung der Warmbewegung der Kristllatome auf Intersitat,
>>> Lage, and
>>> Scharfe der Rontgenspektrallinein, Ann. Physik, 83, 153-183 (1927).
>>>
>>> Interestingly, beta was used for the anisotropic Gaussian form of the
>>> isotropic Gaussian B-factor.
>>>
>>> Bernie
>>>
>>>
>>>
>>> On Wed, January 24, 2007 9:05 am, Roberto Steiner wrote:
>>>> Hi Rajesh,
>>>>
>>>> I also wondered about that.
>>>> Not having been able to find a good explanation in the literature
>>>> I thought of it as reducing factor of the *B*ragg peaks. M???
>>>>
>>>> Then I stopped thinking about it (I now try to call them ADPs)
>>>>
>>>>
>>>> Roberto
>>>>
>>>> On 24 Jan 2007, at 12:42, Rajesh Kumar Singh wrote:
>>>>
>>>>> May be too trivial, I was just wondering
>>>>> what "B" stands for in the term "B-factor".
>>>>>
>>>>> Thanks
>>>>>
>>>>> Rajesh
>>>>>
>>>>> --
>>>>> Rajesh Kumar Singh
>>>>> Institut fur Biochemie
>>>>> Universitat Greifswald
>>>>> Felix-Hausdorff-Str. 4
>>>>> D-17489 Greifswald
>>>>> Germany
>>>>>
>>>>> E.Mail: [EMAIL PROTECTED]
>>>>> Phone: +49-3834- 86 4392
>>>>
>>>> ---
>>>> Dr. Roberto Steiner
>>>> Randall Division of Cell and Molecular Biophysics
>>>> New Hunt's House
>>>> King's College London
>>>> Guy's Campus
>>>> London, SE1 1UL
>>>> Phone +44 (0)20-7848-8216
>>>> Fax   +44 (0)20-7848-6435
>>>> e-mail [EMAIL PROTECTED]
>>>>
>>
>> * * * * * * * * * * * * * * * * * * * * * * * * * * * *
>> Diana R. Tomchick
>> Associate Professor
>> University of Texas Southwestern Medical Center
>> Department of Biochemistry
>> 5323 Harry Hines Blvd.
>> Rm. ND10.214B
>> Dallas, TX 75390-8816, U.S.A.
>> Email: [EMAIL PROTECTED]
>> 214-645-6383 (phone)
>> 214-645-6353 (fax)
>
> * * * * * * * * * * * * * * * * * * * * * * * * * * * *
> Diana R. Tomchick
> Associate Professor
> University of Texas Southwestern Medical Center
> Department of Biochemistry
> 5323 Harry Hines Blvd.
> Rm. ND10.214B
> Dallas, TX 75390-8816, U.S.A.
> Email: [EMAIL PROTECTED]
> 214-645-6383 (phone)
> 214-645-6353 (fax)
>

Re: [ccp4bb] "B" in B-factor

[Santarsiero, Bernard D.]

It looks like the earliest reference to the Debye-Waller factor is from
Debye's paper:

Uber den Einfluss der Warmebewegung uf die Interferenzerscheinungen beiu
Rontgenstrahlen, Verhandl. deut. phyik. Ges., 15, 678-689 (1913),

and the succeeding paper Verhandl. deut. phyik, Ges., 15, 738-752 (1913),

and Waller:

Die Einwirkung der Warmbewegung der Kristllatome auf Intersitat, Lage, and
Scharfe der Rontgenspektrallinein, Ann. Physik, 83, 153-183 (1927).

Interestingly, beta was used for the anisotropic Gaussian form of the
isotropic Gaussian B-factor.

Bernie



On Wed, January 24, 2007 9:05 am, Roberto Steiner wrote:
> Hi Rajesh,
>
> I also wondered about that.
> Not having been able to find a good explanation in the literature
> I thought of it as reducing factor of the *B*ragg peaks. M???
>
> Then I stopped thinking about it (I now try to call them ADPs)
>
>
> Roberto
>
> On 24 Jan 2007, at 12:42, Rajesh Kumar Singh wrote:
>
>> May be too trivial, I was just wondering
>> what "B" stands for in the term "B-factor".
>>
>> Thanks
>>
>> Rajesh
>>
>> --
>> Rajesh Kumar Singh
>> Institut fur Biochemie
>> Universitat Greifswald
>> Felix-Hausdorff-Str. 4
>> D-17489 Greifswald
>> Germany
>>
>> E.Mail: [EMAIL PROTECTED]
>> Phone: +49-3834- 86 4392
>
> ---
> Dr. Roberto Steiner
> Randall Division of Cell and Molecular Biophysics
> New Hunt's House
> King's College London
> Guy's Campus
> London, SE1 1UL
> Phone +44 (0)20-7848-8216
> Fax   +44 (0)20-7848-6435
> e-mail [EMAIL PROTECTED]
>