Re: [ccp4bb] very informative - Trends in Data Fabrication
David Briggs drdavidcbri...@gmail.com a écrit : Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis. Should we say Alea data est or Alea data sunt ? Philippe DUMAS
Re: [ccp4bb] Using intrinsically bound Zn atoms for phasing
A reference for a real MAD phasing with Zinc (worked very well): Ennifar et al. MAD phasing replacing magnesium with zinc. Acta Cryst. (2001). D57, 330 Philippe Dumas Bosch, Juergen jubo...@jhsph.edu a écrit : Since you've collected the data already use your favourite data processing program and treat the Friedel pairs separately. I'd suggest to try HKL2map in conjunction with SHELX C/D/E (sorry for the non CCP4 advertisement here) for solving the heavy atom sites. You can in parallel also try SnB or BnP to find a substructure solution. Depending how bad you resulting density looks like you might want to improve your phases via Sharp. If you want to stay in the CCP4 protected sandbox, then give Crank a try. Jürgen On Mar 6, 2012, at 3:24 PM, Francis E Reyes wrote: http://skuld.bmsc.washington.edu/scatter/AS_form.html Maybe useful to you. However, I would advise to do a fluorescence scan over the range given in the graph and then use chooch to provide the precise energies for your peak and inflection. If you have a large crystal don't expose all of it when you do the fluorescence scan but rather reserve a 'fresh' piece to do your actual data collection. F On Mar 6, 2012, at 1:09 PM, Deepthi wrote: Hi I am trying to solve the structure of an engineered protein.The protein is crystallized with Zn bound to it .We collected a 1.5A0 data. Molecular Replacement didn't yield a good match for the protein. I want to try MAD taking advantage of the Zn atoms in protein. I am not sure what wavelength should i use to collect the diffraction data for Zn. any suggestions? Thank You Deepthi -- Deepthi .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] New Faster-than-fast Fourier transform
George Sheldrick gshe...@shelx.uni-ac.gwdg.de a écrit : For all those interested in the technical details about this new Fourier stuff, I saw that the whole paper is available from the web site, not only the simplified account (look at right of this awfully wrong 3-term Fourier synthesis illutration that I would never show to beginners!) P. Dumas From the rather non-technical inofrmation available so far, it seems to me that it is like leaving out all but the strongest reflections (or perhaps the strongest normalized structure factors). This is unlikely to improve the quality of structure refinement, the importance of using as much data as possible and not leaving out the weakest reflections has often been emphasized. This is quite different to data compression of music. However there is one case where we are already doing this, namely small molecule direct methods or using the same programs to find the heavy atoms in SAD and MAD experiments. These programs use only the strongest 15-20% of the normalized structure factors (E-values). This is possible because the data to parameter ratio is still sufficient, and these reflections contain much of the useful information. However the Fourier routines used by these programs (at least the ones I wrote) are not taking full advantage of the 'sparseness' of the data, so if the MIT people have found a clever way of doing this it might still be useful for heavy atom location (though FFTW and the Intel MKL FFT will be difficult to beat). George On 01/20/2012 06:57 PM, Ethan Merritt wrote: On Friday, 20 January 2012, Jim Fairman wrote: New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html This report is interesting, but it is not immediately obvious to me that crystallographic transforms are in the class of problems for which this algorithm is applicable. From reading the very non-technical article linked above, I conclude that a better summary would be New approach to Fourier approximation provides a very cheap (fast) way of identifying and then discarding components that contribute very little to the signal. In other words, it seems to be a way of increasing the compression ratio for lossy image/audio compression without increasing the amount of time required for compression. So if you're doing map fitting while listening to streamed mp3 music files, perhaps your map inversion will get a slightly larger slice of the CPU time relative to LastFM. On the other hand, it is possible that somewhere in here lies a clever approach to faster solvent flattening. Ethan Philippe DUMAS, responsable d'équipe Directeur de Recherche au CNRS Equipe de Biophysique Biologie Structurale Unité 'Architecture Réactivité de l'ARN', UPR9002 Institut de Biologie Moléculaire et Cellulaire 15, rue René Descartes F67084 STRASBOURG +33 (0)388 41 70 02 http://www-ibmc.u-strasbg.fr/arn/Dumas/index_dum_fr.html
Re: [ccp4bb] how to quantitate protein which dont have ne aromatic residue
Michael Thompson mi...@chem.ucla.edu a écrit : There is a very simple and very quick method that yields an answer approx. 15% reliable: measuring the increment of index of refraction due to the protein. The measurement of an index of refraction can be very accurate. You only need something like a 5µl drop at 1 mg/ml (the order of magnitude should be correct...). Unfortunately, a refractometer is not common in biology labs, but this is a very valuable method. The link between the increment of index of refraction and the protein conc. can be found easily on the web. Philippe Dumas It is not surprising that your bradford and BCA assays don't agree if you have no aromatic amino acids in your protein. Bradford dye binds to hydrophobic residues, mainly aromatics, so I would guess your bradford is consistantly giving lower measurements than the BCA assay. I also wouldn't be surprised if the results of your Bradford vary significantly between replicates. The BCA assay reagent interacts with the backbone amides, not with any sidechains, so I would tend to believe that measurement more than anything else you have done. I work with a protein that has very few hydrophobics (only one aromatic - a Phe) and I have found that Bradfords are unreliable, but the BCA assay tends to be consistent. Mike - Original Message - From: Arpit Mishra ar...@igib.in To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, April 9, 2011 2:52:21 AM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] how to quantitate protein which dont have ne aromatic residue hello everybody i am working on the protien which dont have any aromatic residue i do fplc other purification using 220 absorption, but i want to quantitate protein precisely i have tried using BCA nd bradford but both methods quantification is not matching,,so any one is having sum idea how to quantitate it precisely thanks in advance for your valuable suggestion.. Arpit Mishra -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Fw: Re: [ccp4bb] Solidarity with Japan
Le 16/03/2011 17:59, REX PALMER a écrit : Would it be possible to get information through the CCP4BB about colleagues who do not answer mails ? I'd like to have news about TAKENAKA Akio, Faculty of Pharmacy, Iwaki Meisei University, Tokyo Institute of Technology. Thank you if somebody can transmit the information. Philippe Dumas I was very relieved to learn that my friend and colleague Hideaki Niwa who took his MSc and PhD with me at Birkbeck is safe and well in Japan. I believe that International the Red Cross is doing great work out there and need all the help they can get. You can donate by going to the link below: http://clicks.aweber.com/y/ct/?l=7vf_Vm=1adA9w4Zgg1yh1b=_szL3OnaO1I3NyRX06YTVA http://clicks.aweber.com/y/ct/?l=7vf_Vm=1adA9w4Zgg1yh1b=_szL3OnaO1I3NyRX06YTVA Rex Palmer Birkbeck College attachment: p_dumas.vcf
Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor
What a funny pleasant piece of discussion ! Given any physical quantity Something, having any kind of dimension (even as awful as inches^2*gallons*pounds^-3) Would it exist any room for a discussion about the dimension of 2*Something ? And what about 1*Something ? Philippe Dumas attachment: p_dumas.vcf
Re: [ccp4bb] images
Jacob, Just for the fun, and for historical exactness... I would rather invoke Laplace for such an argumentation, whereas Poincaré should better be invoked for a very strong warning against it. Therefore, ignoring the warning and following Laplace, we could even readily extend your suggestion from back-calculating the images to solving the corresponding structures (and thus also writing the corresponding papers). And write The End (as nauseam, of course ::)) Philippe Dumas Jacob Keller a écrit : Perhaps we could use Poincare's argument(?), that knowing one cross section of the universe in all of its detail would allow forward and back-calculation of all previous states. Then the universe would be its own lab notebook/ archive, and we would not need to bother with all of these technicalities in the first place. The images, then, could be back-calculated from the current (or any) configuration of all the universe's atoms, and then we could work better on improving our crystallography software (and ferreting out fraud) from those... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** begin:vcard fn:Philippe Dumas n:Dumas;Philippe org:CNRS;Biophysique et Biologie Structurale adr;quoted-printable:15 rue Ren=C3=A9 Descartes;;IBMC;Strasbourg;;67084;France email;internet:p.du...@ibmc.u-strasbg.fr title:Directeur de Recherche tel;work:+33 (0)388 41 70 02 tel;fax:+33 (0)388 60 22 18 url:http://www-ibmc.u-strasbg.fr/arn/Dumas/index_dum_fr.html version:2.1 end:vcard
Re: [ccp4bb] Weakest protein-protein complex crystallised
Continuation about this competition between crystal contacts and biologically-relevant contacts Your example is quite interesting because you were able to make the comparison with different ligand affinities, which is exactly what we would have like to test... I just want to add a comment about a possible kinetic, rather than purely thermodynamic, effect. It may be possible that one cannot really compare the affinity of the ligand with that of the molecule-molecule interaction in the lattice because once a molecule-ligand complex has been incorporated into a growing crystal it may be very rapidly protected against the loss of its ligand (and in our case against the binding of a second ligand). Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] [Philippe DUMAS] -Message d'origine- De : Filip Van Petegem [mailto:[EMAIL PROTECTED] Envoyé : Monday, June 30, 2008 9:01 PM À : Philippe DUMAS Cc : CCP4BB@jiscmail.ac.uk Objet : Re: [ccp4bb] Weakest protein-protein complex crystallised Hi, we've had a similar situation: a protein-peptide complex with a Kd in the nM range crystallized in the same condition as the protein alone, and yielded a structure of a complex (voltage-gated calcium channel beta subunit). The exact crystal contacts turned out to be a bit different, as the peptide would clash with a neighbouring molecule in the lattice. However, a mutant protein that increased the Kd to ca 160nM (as confirmed by ITC), using the same peptide crystallized in the same conditions, but this time not as a complex. This effect was reproducible: the WT consistently crystallized as complex, whereas relatively mild mutants (Kd in 100nM range and worse) only yielded crystals of the apo-protein. Conclusion would be that crystal contacts can break relatively tight protein-protein interactions in the ~100nM range, and that crystal contacts are not always that weak. However, the crystallization conditions themselves (PEGs, non-neutral pH) are likely to affect the binding as well. Cheers Filip Van Petegem On Mon, Jun 30, 2008 at 10:42 AM, Philippe DUMAS [EMAIL PROTECTED] wrote: Hello We have had an interesting example where the crystal packing seems to have won against the biological interaction. This is about a sliding clamp made of a very symmetric homodimer having the shape of a ring (encircling DNA during its replication). This beta-ring had been crystallized alone by the Kuriyan group in P1 (thus there was NCS). In our case, we crystallized it with an additional peptide mimicking the C-term of a polymerase binding to the beta-ring [Burnouf et al, JMB 335(2004) 1187]. We expected a symmetric binding of two peptides/ring (one peptide for each protein in the dimer). However, we observed only one peptide/ring. It turns out that we had obtained exactly the same packing in P1 and that one of the two possible binding sites was engaged in crystal contacts. We estimated the Kd of peptide-ring interaction as being in the µmolar range and that there was only a few percent of beta-rings in crystallization drops being singly occupied. Yet the crystallization process selected this minor species to build crystals with (supposedly) a good crystal packing, rather than finding another crystal packing accomodating the doubly-occupied species present in large excess. Our conclusion was that a very modest gain of ca. 2 kcal/mol in the free energy of interaction of singly-occupied beta-rings was sufficient to account for their selection to build crystals against a great majority of doubly-occupied contaminants. This is exactly the order of magnitude mentioned by Ed Pozharski: a single additional H-bond is enough to account for 2 kcal/mol ! And apparently this may be enough to win against biological interactions. Let us not forget that there are many processes comparable to crystallization in living cell... I hope this story makes sense in the frame of this discussion. Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ed Pozharski Envoyé : Monday, June 30, 2008 4:50 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] Weakest protein-protein complex crystallised The word weak is, of course, relative. Free energy of crystallization is roughly 1-2 kcal/mole of crystal contacts (I think I carried this number from Sir Blundell's book, but quick look at papers by Peter Vekilov's group seems to confirm it - am I wrong on this?). I think that crystal contacts are still much weaker than any interaction of biological importance (perhaps I am wrong on this one too and there are important biological protein-protein interaction with 10mM affinity, but I doubt that they are many
Re: [ccp4bb] birefringent spacegroups
Thank you Ian for the comment ! Apparently, I was a bit too quick in my answer. By the way, my mentioning of Fresnel's theory was of pure historical interest and not at all to say that the whole story was written at that time. I went back to my Born Wolf (some kind of a bible in the optics field) and I am somewhat surprised of not seeing any comment on that topics. May be the comments exist, but implicitly in the cited litterature... Now, I am still wondering whether external stresses on biological crystals could indeed induce such unexpected birefringence. Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ian Tickle Envoyé : Thursday, June 12, 2008 9:20 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] birefringent spacegroups But it seems that Hendrik Lorentz was the first to realise that symmetry breaking of the isotropy of the refractive index other optical properties could occur in cubic crystals at sufficiently short wavelength even in the absence of a distorting force - the spatial-dispersion-induced birefringence effect referred to in the paper. Note that this is an intrinsic effect, it has nothing to do with external stress, electric field etc., and if you read the paper you'll see that such external effects were specifically eliminated as the cause of the observed effect. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Philippe DUMAS Sent: 12 June 2008 19:20 To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] birefringent spacegroups Hello, A short comment of historical interest: the first theory about double refraction in crystals (with explicit calculation of the index ellipsoid) goes back to 3 memoirs by A. Fresnel in 1821 and 1822. So, we are even in older regions. This being said, in cubic crystals the index ellipsoid can only be a sphere. An so, no birefringence should exist (unless there is some external cause of anisotropy: mecanical stress, electric field,...). See Born Wolff (principles of optics) p. 703. May be, our biological crystals might quite easily develop such stress birefringence... Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ian Tickle Envoyé : Thursday, June 12, 2008 7:19 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] birefringent spacegroups PS in case you missed it, here's the bottom line from the paper: Interestingly, a cubic crystal has seven nonbirefringent axes, four in the 111 directions and three in the 100 directions, with birefringence maxima in the twelve 110 directions. So it would appear that the optical properties of cubic crystals are *more* complicated than those of lower symmetry systems, not less! - and previous conclusions about isotropy of cubic crystals probably arose because the measurements were simply not precise enough (or not carried out at short enough wavelength) to detect the effect. However the relevant theory goes back to Lorentz (1878) so it's not exactly new! Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: 12 June 2008 17:50 To: Ethan A Merritt; Jacob Keller Cc: CCP4BB@jiscmail.ac.uk Subject: RE: [ccp4bb] birefringent spacegroups Hi Ethan You could be right, see this paper: http://physics.nist.gov/Divisions/Div842/Gp2/DUVMatChar/PDF/In tBiref.pdf Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt Sent: 12 June 2008 15:46 To: Multiple recipients Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] birefringent spacegroups On Wednesday 11 June 2008 23:55, Robin Owen wrote: Hi Jacob, The birefringence of a crystal is determined by a three dimensional shape (the indicatrix) describing how refractive index varies with direction within the crystal. You can think of this as a 3d ellipse and the birefringence is given by the difference in length of the two axes of the ellipse 'seen' by light as it passes through the crystal. The orientation and shape of the indicatrix are constrained by the point group symmetry of the crystal. In the case of cubic crystals, the indicatrix is characterised by four 3-fold axes. The indicatrix for all cubic crystals is thus a sphere and cubic crystals are non-birefringent. Hexagonal, trigonal and tetragonal crystals are uniaxial and the indicatrix is an ellipsoid of revolution - there is one direction in which the crystal appears non-birefringent. Orthorhombic, monoclinic
Re: [ccp4bb] Help with Superpose results
Although this is not a very important issue..., I am a bit surprised by
Gerard's insistance for a 'stop calling rmsd rms deviation'. Isn'it a
general term in statistical studies, valid for distances separating
homologous atoms as well as for any other factor (B factors for example) ?
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue Rene Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de
Gerard DVD Kleywegt
Envoye : Monday, April 07, 2008 7:20 PM
A : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
Is the rms xyz displacement equivalent to an rmsd??
yes. it is in fact a better name than rms deviation, although i think
'root-mean-square distance' is even better, as it says exactly what you
calculate.
think of it like this, the formula for rmsd is:
RMSD = square-root [ SUM(atoms) { (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 } /
Natoms
]
now, (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 is the Square of the Distance
between
two equivalenced atoms in structure 1 and 2; adding them for all pairs of
equivalenced atoms and dividing by the number of atoms gives you the Mean
Squared Distance; finally, taking the square root yields the
Root-Mean-Square
Distance, or RMSD
so, people, can we all please stop calling rmsd rms deviation - it really
is
an rms distance (or rms displacement). you could argue that the formula
gives some kind of rms coordinate deviation, but in that case you ought to
divide by 3*Natoms instead.
(having said that, the term RMS B displacement sounds positively silly!)
--dvd
**
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
**
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
**
Re: [ccp4bb] Help with Superpose results
Apparently I had missed some subtle considerations...
Yet, I confess am not fully convinced: is it so wrong to speak of how much
different structures DEVIATE from each other ? I do not see what prevents
you from defining the correct underlying probability distribution. That
interatomic distances can be used to quantify deviations does not hurt me so
much.
Thank you anyway...
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue René Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : Ed Pozharski [mailto:[EMAIL PROTECTED]
Envoyé : Tuesday, April 08, 2008 3:56 PM
À : Philippe DUMAS
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
RMS deviation refers to the variance of a random variable - it is a
characteristic of the underlying probability distribution. When you
superpose two different structures, you are looking at the DISTANCE
between atoms, not the DEVIATION in their position. In fact, for
individual atoms you can't even say root-mean-square, it's just plain
distance. The core argument is that you are looking at two structures
that represent different underlying probability distributions, and so
it's definitely not the rms deviation you are calculating, but rms
distance (rms over all the atoms in the structure). HTH,
Ed.
On Tue, 2008-04-08 at 11:07 +0200, Philippe DUMAS wrote:
Although this is not a very important issue..., I am a bit surprised by
Gerard's insistance for a 'stop calling rmsd rms deviation'. Isn'it a
general term in statistical studies, valid for distances separating
homologous atoms as well as for any other factor (B factors for example) ?
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue Rene Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de
Gerard DVD Kleywegt
Envoye : Monday, April 07, 2008 7:20 PM
A : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
Is the rms xyz displacement equivalent to an rmsd??
yes. it is in fact a better name than rms deviation, although i think
'root-mean-square distance' is even better, as it says exactly what you
calculate.
think of it like this, the formula for rmsd is:
RMSD = square-root [ SUM(atoms) { (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 } /
Natoms
]
now, (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 is the Square of the Distance
between
two equivalenced atoms in structure 1 and 2; adding them for all pairs of
equivalenced atoms and dividing by the number of atoms gives you the Mean
Squared Distance; finally, taking the square root yields the
Root-Mean-Square
Distance, or RMSD
so, people, can we all please stop calling rmsd rms deviation - it
really
is
an rms distance (or rms displacement). you could argue that the
formula
gives some kind of rms coordinate deviation, but in that case you ought to
divide by 3*Natoms instead.
(having said that, the term RMS B displacement sounds positively silly!)
--dvd
**
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
**
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
**
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /
Re: [ccp4bb] radiation damage question
Yes indeed ! H2 is one product of H2O radiolysis by recombination of two H radicals. Whether or not the cleavage of iodine (quite efficient under X-rays) is a factor increasing H2 production, I don't know. Philippe Dumas IBMC-CNRS, UPR9002 15, rue Rene Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Patrick Loll Envoye : Monday, March 03, 2008 6:00 PM A : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] radiation damage question Hi all, I had an interesting experience, and wonder if others have seen similar things. I was collecting data from a crystal that contains an iodinated macromolecule. After 2 days on a copper rotating anode, with the crystal at 100 K, we experienced a detector problem, so I put the crystal back into the dewar; it was diffracting nicely when I took it off. For various reasons, I didn't get back to this crystal until about 3 weeks later. When I put it back on the goniostat, the mother liquor was milky white in appearance. There were no ice rings, but alas the crystal only gave a few anemic spots around the beamstop. Annealing didn't help, and I noticed that when I blocked the cold stream, the milky white appearance didn't go away when the sample thawed. I finally took the crystal off and looked at it under a microscope, at which point I discovered that the milky white appearance was due to the presence of bubbles in the mother liquor. I seem to recall some talks on radiation damage in which people mention the evolution of a gas (H2?). So: Does this seem like a radiation damage phenomenon? And have others seen this kind of delay in the manifestation of damage during storage at liquid N2 temperatures? Thanks, Pat -- - Patrick J. Loll, Ph. D. (215) 762-7706 Professor FAX: (215) 762-4452 Department 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 [EMAIL PROTECTED]
Re: [ccp4bb] CCP4 rotation convention
Just my own amount of salt in the Rotation function soup... I just want to try defending the poor little Euler angles. First, Euler invented them... Yes ! Second, only Euler angles yield a very nice interpretation of Rot Funct symmetry in terms of space group. See the two venerable papers: Tollin, Main Rossmann, Acta Cryst 20 (1966) 404 and Narasinga, Jih Hartsuck, Acta Cryst A36(1980) 878 Third, only Euler angles yield a very practical and intuitive thing, namely it does not matter rotating by (alpha, beta,gamma) in the usual way, or first, prerotating by gamma around Z (but without rotating any axes !) and then making the alpha rotation around Z (rotating now the axes) followed by the beta rotation around the new Y. This is most easily seen with a cylinder that one rotates in the two ways. Last, the inverse rotation matrix of the Euler matrix defined by (alpha, beta, gamma) is just the Euler matrix defined by (-gamma, -beta, -alpha). Ian, isn't worth the effort ? Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ian Tickle Envoyé : Monday, August 13, 2007 8:11 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] CCP4 rotation convention Hi folks I hate to say this but I think everyone here has got it wrong to some degree (including myself - and I hereby retract my previous e-mail and issue the correction below!). If you don't believe me then read digest Jorge Navaza's article Rotation functions in Int. Tab. Vol. F (sect 13.2, p. 269), particularly sections 13.2.2 and Appendix A13.2.1.1. Phil's article in Acta D57 1355-1359 (2001), i.e. the 2001 S/W proceedings, states: ... the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around the new z again, R = Rz'(a).Ry'(b).Rz(g) Compare this with Jorge's equation 13.2.2.3 which he explicitly states applies to rotations about fixed axes, not rotated axes (but using my notation): R = Rz(a).Ry(b).Rz(g) i.e. first by gamma about z, then by beta about the *fixed* y axis, then by alpha about the *fixed* z axis. The same formula cannot apply to both rotations about fixed and rotated axes at the same time! Looking at Jorge's equation 13.2.2.1 it's plain that the correct version involving rotated axes is (again substituting my own notation which should be obvious): R = Rz'(g).Ry'(b).Rz(a) i.e. the correct statement is that the rotation is generated by rotating first by alpha about z, then by beta about the rotated y axis (y'), then by gamma about the rotated z axis (z'). Of course it may well be that Phil's equation is based on an older version of Jorge's analysis perhaps using a different convention in his Acta Cryst. (1994), A50, 157-163 paper, but unfortunately I don't have online access to AC(A) to check it out, maybe someone who has access could do so. In fact it's quite obvious looking at the individual matrices Rz(a) Ry(b) at the bottom of page 1358 in Phil's paper that they must apply to fixed not rotating axes, because if say the Ry(b) matrix were for rotation about the rotated y axis, it would have to be a function of gamma: applying the Rz(g) matrix as given in the paper first to the y-axis vector (0,1,0) gives the rotated y-axis vector (-sin(g),cos(g),0). Similarly if the Rz(a) matrix represented rotation about the rotated z axis it would have to be a function of both beta gamma and plainly it's not. This all goes to show that a) even the experts sometimes get it wrong particularly where matrix algebra is concerned, and b) you should avoid the concept of rotating about rotated axes like the plague! -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: 12 August 2007 20:37 To: CCP4BB@JISCMAIL.AC.UK Subject: CCP4 rotation convention Dear programmers - Phil Evans writes in acta D57 1355 (2001) on p 1358 section 5.2: the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around the new z again, R = Rz(al)Ry(be)Rz(ga) This seems correct, as the first rotation is applied first to vector x, then the second to the new one, etc, thus x' = (Rz(al)(Ry(be)(Rz(ga)x))) In J.Appl.Cryst. 30 402-410 (1977) in the convrot description, Sascha Uzhumtsev lists in table one for (Navaza 1994): alpha about Z, beta about Y and gamma about new Z and gives the *same* resulting rotation Rz(al)Ry(be)Rz(ga) This seems to be a contradiction I cannot resolve? Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL
[ccp4bb] Post-doc position
Postdoc position in Protein-RNA crystallography A postdoc position is available in the group of crystallography headed by P. Dumas in the laboratory RNA Architecture and Reactivity at IBMC, Strasbourg (France). The position is for an HIV-related project that will focus on the structure of a ternary complex between (1) a tRNA(Lys,3) (diverted from the infected cell), (2) a fragment of the viral RNA and (3) the viral retrotranscriptase (RT). The formation of this ternary complex is a key step in the viral replication cycle since it occurs early and involves a cellular partner (the tRNA(Lys,3)) that is independent of any viral mutations. For that reason, it might be an excellent target for a new antiviral drug. The structural work will benefit strongly of a large body of previous solution studies. In particular, a selenomethionine viral RT, the tRNA(Lys,3), as well as viral RNA fragments of various lenght are routinely produced in our lab. We are equipped with a crystallization robot and with an X-ray facility for crystal testing. Our laboratory is located into a thriving environment for all aspects of RNA research. Qualification: The candidate should have a PhD with a background in RNA biology. An experience in X-ray crystallography will be strongly appreciated. How to apply: send a CV with a list of publications to Eric Ennifar: [EMAIL PROTECTED] Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED]
