Re: [ccp4bb] inflated BOND_RMSD with external restraints (refmac)
Ed, On a practical side, I now have a misleading bond_rmsd value. The correct one can be calculated as described, but this may make geometry weight optimization cumbersome. Do I understand correctly that an alternative is to monitor Zbonds, with a rule that it should be around 1.0? No, the average value of Zbonds over the whole PDB is almost exactly 0.5 (there's no clear resolution-dependence), so that would be a good starting point. Re-refinement of ~98% of the PDB (PDB-REDO project) using weight optimisation showed a linear dependence of Zbonds on resolution in the resolution range 1 to 3 Ang.: Zbonds = 0.85 - 0.146*dmin (SD = 0.2) so e.g. Zbonds = 0.56 @ 2 Ang. Cheers -- Ian And more generally, shouldn't we not look at rmsd_bonds at all and only use Zbonds instead (which is, I assume, an average bond length deviation to the target value ratio?) Correct. I suspect that acceptable bond_rmsd value is slightly affected by sequence. Not really, the effect of sequence on the bond lengths is insignificant in comparison with the uncertainty. Cheers -- Ian
Re: [ccp4bb] inflated BOND_RMSD with external restraints (refmac)
And more generally, shouldn't we not look at rmsd_bonds at all and only use Zbonds instead (which is, I assume, an average bond length deviation to the target value ratio?) Sorry, I just realised that I misread what you wrote (that's what comes of speed-reading!). What you said above is NOT correct: yes you should monitor Zbonds, but Zbonds is defined in (almost) the usual way for a statistical RMS(Z-score), i.e. it's the RMS value of: Z' = (deviation of observed from target value) / (standard uncertainty of the target value). I say 'almost' because it's not a true Z-score which would be defined as: Z = (deviation of observed from target value) / (standard uncertainty of the deviation) The expected value of Z^2 is 1 as you say, the expected value of Z'^2 is not (it's always 1). Unfortunately we can't easily calculate the true Z-score: the deviation in question is (dobs - dtarg); the standard uncertainty of this cannot easily be calculated. We know SU(dtarg) but we don't know SU(dobs) and most importantly we don't know COV(dobs,dtarg) (dobs and dtarg are obviously not independent so we cannot even assume that the covariance is zero). -- Ian
Re: [ccp4bb] vector and scalars
On 10/14/10 11:22, Ed Pozharski wrote: Again, definitions are a matter of choice There is no correct definition of anything. Definitions are a matter of community choice, not personal choice; i.e. a matter of convention. If you come across a short squat animal with split hooves rooting through the mud and choose to define it as a giraffe, you will find yourself ignored and cut off from the larger community which chooses to define it as a pig. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] inflated BOND_RMSD with external restraints (refmac)
Garib, indeed - I tested 5.6.077 and the bond_rmsd is down to 0.006 as it should. Thanks, Ed. On Thu, 2010-10-14 at 22:04 +0100, Garib N Murshudov wrote: Hi Ed refmac 5.6 should not have this problem. Yes, you are right. It should be considered as a bug. I think I have fixed it. Could you please try 5.6version from: www.ysbl.york.ac.uk/refmac/latest_refmac.html You need to take experimental version (it should be stable enough, although I update it more often than older versions). In this version to make external restraints as covalent bonds you need to specify type 1 (type 0 means dictionary values will be overwritten and type 2 is external restraints for non-covalent bonds) I hope it helps regards Garib On 14 Oct 2010, at 21:51, Ed Pozharski wrote: It appears that external restraints are included in bond_rmsd calculation. When they are used to restrain the hydrogen bonds to maintain the Watson-Crick pairing in a 3A resolution structure of a protein-DNA complex, the bond_rmsd is inflated about 5 times. To verify this, the refmac run was done with external restraints removed and zero refinement cycles. With external restraints I get 0.028A, without - 0.006A. This is with v.5.5.0109. I assume this may be classified as a bug - there is no limitation to using external restraints only for the covalent bonds, thus they should not be included in bond_rmsd calculation. On a practical side, I now have a misleading bond_rmsd value. The correct one can be calculated as described, but this may make geometry weight optimization cumbersome. Do I understand correctly that an alternative is to monitor Zbonds, with a rule that it should be around 1.0? And more generally, shouldn't we not look at rmsd_bonds at all and only use Zbonds instead (which is, I assume, an average bond length deviation to the target value ratio?) I suspect that acceptable bond_rmsd value is slightly affected by sequence. Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs -- 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] vector and scalars
As usual, the Omniscient Wikipedia does a pretty good job of giving the standard mathematical definition of a vector: http://en.wikipedia.org/wiki/Vector_space#Definition If the thing fulfills the axioms, it's a vector. Complex numbers do, as well as scalars. On Oct 15, 2010, at 8:56 AM, David Schuller wrote: On 10/14/10 11:22, Ed Pozharski wrote: Again, definitions are a matter of choice There is no correct definition of anything. Definitions are a matter of community choice, not personal choice; i.e. a matter of convention. If you come across a short squat animal with split hooves rooting through the mud and choose to define it as a giraffe, you will find yourself ignored and cut off from the larger community which chooses to define it as a pig. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Assistant Professor Department of Biochemistry Mailstop 009 415 South St Brandeis University Waltham, MA 02454-9110 dtheob...@brandeis.edu http://theobald.brandeis.edu/ Office: +1 (781) 736-2303 Fax:+1 (781) 736-2349 ^\ /` /^. / /\ / / /`/ / . /` / / ' ' ' smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] vector and scalars
Douglas, The elements of a 'vector space' are not 'vectors' in the physical sense. The correct Wikipedia page is this one http://en.wikipedia.org/wiki/Euclidean_vector Ganesh On Fri, 15 Oct 2010 11:20:04 -0400, Douglas Theobald dtheob...@brandeis.edu wrote: As usual, the Omniscient Wikipedia does a pretty good job of giving the standard mathematical definition of a vector: http://en.wikipedia.org/wiki/Vector_space#Definition If the thing fulfills the axioms, it's a vector. Complex numbers do, as well as scalars. On Oct 15, 2010, at 8:56 AM, David Schuller wrote: On 10/14/10 11:22, Ed Pozharski wrote: Again, definitions are a matter of choice There is no correct definition of anything. Definitions are a matter of community choice, not personal choice; i.e. a matter of convention. If you come across a short squat animal with split hooves rooting through the mud and choose to define it as a giraffe, you will find yourself ignored and cut off from the larger community which chooses to define it as a pig. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] vector and scalars
On Oct 15, 2010, at 11:37 AM, Ganesh Natrajan wrote: Douglas, The elements of a 'vector space' are not 'vectors' in the physical sense. And there you make Ed's point -- some people are using the general vector definition, others are using the more restricted Euclidean definition. The elements of a general vector space certainly can be physical, by any normal sense of the term. And note that physical 3D space is not Euclidean, in any case. The correct Wikipedia page is this one http://en.wikipedia.org/wiki/Euclidean_vector Ganesh On Fri, 15 Oct 2010 11:20:04 -0400, Douglas Theobald dtheob...@brandeis.edu wrote: As usual, the Omniscient Wikipedia does a pretty good job of giving the standard mathematical definition of a vector: http://en.wikipedia.org/wiki/Vector_space#Definition If the thing fulfills the axioms, it's a vector. Complex numbers do, as well as scalars. On Oct 15, 2010, at 8:56 AM, David Schuller wrote: On 10/14/10 11:22, Ed Pozharski wrote: Again, definitions are a matter of choice There is no correct definition of anything. Definitions are a matter of community choice, not personal choice; i.e. a matter of convention. If you come across a short squat animal with split hooves rooting through the mud and choose to define it as a giraffe, you will find yourself ignored and cut off from the larger community which chooses to define it as a pig. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] vector and scalars
As usual, the Omniscient Wikipedia does a pretty good job of giving the standard mathematical definition of a vector: http://en.wikipedia.org/wiki/Vector_space#Definition If the thing fulfills the axioms, it's a vector. Complex numbers do, as well as scalars. It is a bit more complicated, unfortunately. cf: http://en.wikipedia.org/wiki/Complex_number#The_complex_plane http://en.wikipedia.org/wiki/Complex_number#Real_vector_space
Re: [ccp4bb] vector and scalars
Maybe this will shed insight into the problem: What do you get when you cross a mosquito with a rock climber? Nothing. You can't cross a vector and a scalar Have a good weekend, JPK
Re: [ccp4bb] vector and scalars
On Oct 15, 2010, at 12:14 PM, William G. Scott wrote: As usual, the Omniscient Wikipedia does a pretty good job of giving the standard mathematical definition of a vector: http://en.wikipedia.org/wiki/Vector_space#Definition If the thing fulfills the axioms, it's a vector. Complex numbers do, as well as scalars. It is a bit more complicated, unfortunately. cf: Don't you mean, it's a bit more _complex_? :) http://en.wikipedia.org/wiki/Complex_number#The_complex_plane http://en.wikipedia.org/wiki/Complex_number#Real_vector_space smime.p7s Description: S/MIME cryptographic signature
[ccp4bb] quantum diffraction
Oh dear, here we go again. I know that there are people out there who have a hard time accepting quantum mechanics, but yes, each photon really does interact with EVERY ELECTRON IN THE CRYSTAL at once. Young's double-slit experiment is the simplest form of diffraction, which he performed in 1801 to settle an argument about the wave vs particle nature of light. The tricky bit, however, was performing the experiment at such low flux that only one particle is in flight at any given moment (Dontai et al. 1973, done with electron diffraction). However, if you do this, you still get an interference pattern at the end of the day: http://en.wikipedia.org/wiki/File:Double-slit_experiment_results_Tanamura_2.jpg This is the observation, and Mother Nature doesn't care if we like it or not. The only way we can interpret it is to conclude that the photon must be interfering with itself. In fact, anyone with a Pilatus detector (and a lot of extra beam time) can verify the self-interference of photons in macromolecular crystal diffraction. Since the source-to-detector distance of a typical MX beamline is about 30 m, it takes 100 nanoseconds for a photon generated in the storage ring to fly down the beam pipe, do whatever it is going to do in the crystal, and then (perhaps) increment a pixel on the detector. So, as long as you keep the time between photons much greater than 100 nanoseconds you can be fairly confident that there is never more than one photon anywhere in the beamline at a given instant. Now, one photon per 100 nanoseconds is 1e7 photons/s, which is a pretty weak flux for an MX beamline, but not too bad. Ideally, of course, one would want to read out images from the Pilatus that contain at most one photon hit each. You would then sum these images all together after the experiment to confirm that you do, in fact, get the same diffraction pattern that you would have gotten using higher flux. I am willing to take bets on this! Then again, this is exactly how the old multi-wire detectors worked (at much lower flux). So, I suppose this experiment has already been done? The other observation that can only be explained by quantum mechanics is the fact that electrons orbiting atomic nuclei do not emit synchrotron radiation. Amazingly, this latter conclusion was first reached by Debye in the introduction of his now famous paper on temperature factors (Debye, P. J. W. 1915, Annalen der Physik 351, 809-823). http://dx.doi.org/10.1002/andp.19153510606 Yes, this is the paper where Debye first defines what we now call the B-factor (although he doesn't use B), as well as the first occurrence of the Lorentz factor (which appears in a second note-added-in-proof). If you read it (perhaps with the help of Google translate), you can tell that the conclusion about the de-localized nature of electrons in atoms was deeply disturbing to him as well. After all, we are all scientists, and letting go of determinism is not easy. -James Holton MAD Scientist
Re: [ccp4bb] inflated BOND_RMSD with external restraints (refmac)
Thanks, Ian, this is excellent. It appears that depending on the sequence the ideal target rmsd may vary from 0.018 for a poly-H to 0.024 for a poly-P. Except for some really short sequences, in PDB the variation is generally between 0.021-0.022, indeed undetectable. On Fri, 2010-10-15 at 10:26 +0100, Ian Tickle wrote: Ed, On a practical side, I now have a misleading bond_rmsd value. The correct one can be calculated as described, but this may make geometry weight optimization cumbersome. Do I understand correctly that an alternative is to monitor Zbonds, with a rule that it should be around 1.0? No, the average value of Zbonds over the whole PDB is almost exactly 0.5 (there's no clear resolution-dependence), so that would be a good starting point. Re-refinement of ~98% of the PDB (PDB-REDO project) using weight optimisation showed a linear dependence of Zbonds on resolution in the resolution range 1 to 3 Ang.: Zbonds = 0.85 - 0.146*dmin (SD = 0.2) so e.g. Zbonds = 0.56 @ 2 Ang. Cheers -- Ian And more generally, shouldn't we not look at rmsd_bonds at all and only use Zbonds instead (which is, I assume, an average bond length deviation to the target value ratio?) Correct. I suspect that acceptable bond_rmsd value is slightly affected by sequence. Not really, the effect of sequence on the bond lengths is insignificant in comparison with the uncertainty. Cheers -- Ian -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] [QUAR] Re: [ccp4bb] embarrassingly simple MAD phasing question (another)
Actually, people forget the 1/r term because it is gone by the end of Chapter 6 of Woolfson. Yes, it is true that, for the single reference electron the scattered intensity falls off with the inverse square law of distance (r) and, hence, the amplitude falls off with 1/r. However, the units of intensity here is photons/area. This is not the same as the units of intensity for an integrated diffraction spot (photons). That is, spots are an integral over solid angle, so the 1/r^2 term goes away. A shame, really, that we use the word intensity to describe so many different things. Leads to a lot of confusion like this! It is also a real shame that certain individuals are so draconianly eristic about units because this discourages the use of colloquial units (like photons/um^2 or electrons) as an educational tool. The loss of the 1/r^2 term arises because diffraction from a crystal is compressed into very sharp peaks. That is, as the crystal gets larger, the interference fringes (spots) get smaller, but the total number of scattered photons must remain constant. The photons/area at the tippy-top of this transform-limited peak is (theoretically) very large, but difficult to measure directly as it only exists over an exquisitely tiny solid angle at a very precise still crystal orientation. In real experiments, one does not see this transform-limited peak intensity because it is blurred by other effects, like the finite size of a pixel (usually very much larger than the peak), the detector point-spread function, the mosaicity of the crystal, unit cell inhomogeneity (Nave disorder) and the spread of angles in the incident beam (often called divergence or crossfire). It is this last effect that often tricks people into thinking that spot intensity falls off with 1/r. However, if you do the experiment of chopping down the beam to a very low divergence, choosing a wavelength where air absorption is negligible, and then measuring the same diffraction spot at several different detector distances you really do find that the pixel intensity is the same: independent of distance. Yes, I have actually done this experiment! -James Holton MAD Scientist On 10/14/2010 8:33 PM, William G. Scott wrote: On Oct 14, 2010, at 2:28 PM, Jacob Keller wrote: I have always found this angle independence difficult. Why, if the anomalous scattering is truly angle-independent, don't we just put the detector at 90 or 180deg and solve the HA substructure by Patterson or direct methods using the pure anomalous scattering intensities? Or why don't we see pure anomalous spots at really high resolution? I think Bart Hazes' B-factor idea is right, perhaps, but I think the lack of pure anomalous intensities needs to be explained before understanding the angle-independence argument. JPK Yo Jacob: I think one thing that got ignored as I followed the other irrelevant tangent is what f and F are. f is the atomic scattering factor, and F is the corresponding Fourier sum of all of the scattering centers. This holds for f_0 vs. F_0, f' vs. F' and f vs. F. The spots we are measure correspond to the capital Fs. Just like we add the f_o for each scatterer together and we get a sum (F) that has a non-zero phase angle, this also holds for F (that is the part I missed when I posted the original question my student asked me). The full scattered wave isn't given by f by the way. It is (1/r) * f(r) * exp(ikr) so the intensity of the scattered wave will still tail off due to the that denominator term (which is squared for the intensity). That holds for f_o, f' and f unless I missed something fundamental. People tend to forget that (1/r) term because we are always focusing on just the f(r) scattering factor. -- Bill
Re: [ccp4bb] vector and scalars
I couldn't resist: What do you get when you cross an elephant with an orange? Elephant.orange.sin(theta) Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Fri, 15 Oct 2010, Jacob Keller wrote: Maybe this will shed insight into the problem: What do you get when you cross a mosquito with a rock climber? Nothing. You can't cross a vector and a scalar Have a good weekend, JPK
[ccp4bb] update REFMAC
To upgrade the Refmac version that I am running from inside the CCP4i, I did the following mv $CCP4/bin/refmac5 $CCP4/bin/refmac5.5 cp refmacgfortran $CCP4/bin/refmac5.6 ln -s $CCP4/bin/refmac5.6 $CCP4/bin/refmac5 It seems to have worked fine. Is there more intelligent way of doing this? -- 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 /
[ccp4bb] Source for trimethyl lead acetate
Our supplies of trimethyl lead acetate are running low. Does anybody know of a chemical supplier that still makes it. Matthew Vetting
Re: [ccp4bb] quantum diffraction
but yes, each photon really does interact with EVERY ELECTRON IN THE CRYSTAL at once. Take a crystal from the cave...10m long..perhaps not 'really'... It is however helpful to think of a coherence volume of the photon in which it interacts with every atom. We had some discussions and estimates before, and starting from transition lifetime we ended up with an estimated 'single photon coherence length' of a several 1000 A to several 10um or so on synchrotron sources. These numbers at least seem reasonable and are not contradicting any practical observations. What 'really' happens depends on your definition of realityI like the photon annihilation- creation picture, but in condensed multi-particle matter that also stretches at least my imagination... Best, BR
Re: [ccp4bb] quantum diffraction
but yes, each photon really does interact with EVERY ELECTRON IN THE CRYSTAL at once. Take a crystal from the cave...10m long..perhaps not 'really'... It is however helpful to think of a coherence volume of the photon in which it interacts with every atom. We had some discussions and estimates before, and starting from transition lifetime we ended up with an estimated 'single photon coherence length' of a several 1000 A to several 10um or so on synchrotron sources. These numbers at least seem reasonable and are not contradicting any practical observations. What 'really' happens depends on your definition of realityI like the photon annihilation- creation picture, but in condensed multi-particle matter that also stretches at least my imagination... Best, BR *** 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 ***
Re: [ccp4bb] Source for trimethyl lead acetate
Hi Matthew, Try http://www.scbt.com/datasheet-233809-acetoxytrimethyllead-iv.html Cheers, Martin On Oct 15, 2010, at 7:54 PM, matthew vetting wrote: Our supplies of trimethyl lead acetate are running low. Does anybody know of a chemical supplier that still makes it. Matthew Vetting . Martin Hallberg, PhD Department of Cell and Molecular Biology Karolinska Institutet Stockholm Sweden http://tinyurl.com/yzn9y5j
Re: [ccp4bb] quantum diffraction
On 10-10-15 10:37 AM, James Holton wrote: ... In fact, anyone with a Pilatus detector (and a lot of extra beam time) can verify the self-interference of photons in macromolecular crystal diffraction. Since the source-to-detector distance of a typical MX beamline is about 30 m, it takes 100 nanoseconds for a photon generated in the storage ring to fly down the beam pipe, do whatever it is going to do in the crystal, and then (perhaps) increment a pixel on the detector. So, as long as you keep the time between photons much greater than 100 nanoseconds you can be fairly confident that there is never more than one photon anywhere in the beamline at a given instant. ... Does the length of the beamline really matter? As long as the photons are spaced apart more than the coherence length (several 1000 A to several 10um on a synchrotron beamline according to Bernard's post) they should be considered independent events. So the photon rate can probably be 5 to 6 orders of magnitude higher while still doing single photon diffraction experiments. Bart -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521
Re: [ccp4bb] quantum diffraction
btw, buckyballs have measurable wave properties. i think they are trying virus particles now.
Re: [ccp4bb] quantum diffraction
On 10/15/10 12:38, Bart Hazes wrote: The photon moves through the crystal in finite time and most of the time it keeps going without interacting with the crystal, i.e. no diffraction. However, if diffraction occurs it is instantaneous, or at least so fast as to consider it instantaneous. In some cases a diffracted photon diffracts another time while passing through the remainder of the crystal. Or in Ruppian terms, a poof-pop-poof-pop event. If you listen carefully you may be able to hear it. The photon both diffracts and doesn't diffract as it passes through the crystal and it diffracts into all the directions that match the Bragg condition. The wave function doesn't collapse to a single outcome until the detector measures something - which in the scheme of things occurs long after the photon left the crystal. The photon also interacts with the electrons for as long as the wave functions overlap. You have to solve the time-dependent Schrodinger equation to get the details. In all the the QM classes I've had they start by writing the time-dependent equation and then immediately erasing it - never to be mentioned again. All the rest of the term was spent with the time-independent equation and the approximation of the instantaneous quantum jump. If you assume that nothing changes with time the only way to model changes is with discontinuities. Dale Bart On 10-10-15 12:43 PM, Jacob Keller wrote: but yes, each photon really does interact with EVERY ELECTRON IN THE CRYSTAL at once. A minor point: the interaction is not really at once, is it? The photon does have to move through the crystal over a finite time. JPK
Re: [ccp4bb] quantum diffraction
Arndt, M.; O. Nairz, J. Voss-Andreae, C. Keller, G. van der Zouw, A. Zeilinger (14 October 1999). Wave-particle duality of C60. Nature 401: 680-682. doi:10.1038/44348. They came up with 2.5 pm for the C60. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bryan Lepore Sent: Friday, October 15, 2010 1:07 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] quantum diffraction btw, buckyballs have measurable wave properties. i think they are trying virus particles now.=
Re: [ccp4bb] quantum diffraction
On 10-10-15 02:14 PM, Dale Tronrud wrote: ... The photon both diffracts and doesn't diffract as it passes through the crystal and it diffracts into all the directions that match the Bragg condition. The wave function doesn't collapse to a single outcome until the detector measures something - which in the scheme of things occurs long after the photon left the crystal. ... and On 10-10-15 02:07 PM, Bryan Lepore wrote: btw, buckyballs have measurable wave properties. i think they are trying virus particles now. That reminds me that politicians also have wave properties photons interact with electrons their diffraction leads to interference for most angles the results cancel out when they are not on a common wavelength you get Laue diffraction their is no single outcome until the detector measures something politicons interact with the electorate their diffrent fractions lead to interference on most angles the results cancel out when they are not on a common wavelength you get loud distraction there is no single outcome until the polls measure something Bart -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521
Re: [ccp4bb] crystal growth
If I remember correctly, NaF forms octahedral crystals. Be sure to check for salt crystals in your reservoir well. ho
[ccp4bb] peculiar twinning case
A couple of twinning-related questions. I have a protein-DNA complex in P65. Protein binds DNA as a dimer, DNA itself is not palindromic and has sticky ends located asymmetrically with respect to the protein (dimer). DNA contains a single fluoro-uracil which is flipped into the active site. This 3A structure can be easily refined down to Rf~35%, at which point difference density tracing the fluoroU and adjacent basepairs of a self-superimposed dimer is visible in the active site of the second monomer. The dimer two-fold axis are aligned with the bisector of the (a,b). Thus my first question - do I understand correctly that this corresponds exactly to (k,h,-l) operator which is one of the possible twinning operators in P65? When I try twin refinement in Refmac, the Rfree drops some 3% and reported twinning fraction is 10%. It's great to have the lower Rfree, of course, but I doubt that 10% occupancy would give me a detectable density (I see mainly phosphate, but the fluoro-U moiety is rather clear too). And indeed, the difference density remains after accounting for twinning. So I tried the dual model, where I have two copies of the whole assembly, with the second one obtained by rotation around dimer axis. The Rfree drops another 3%, and the difference density is now accounted for, but the occupancy optimized for the lowest Rfree is about 50%. Thus my second question - since twinning appears to be related to the same spatial transformation, why it doesn't account for it? And in more general sense - what is going on in this lattice? Afaiu, the twinning and dual model contribute to the Fc in different ways. For twinning part, the Fc=sqrt(|F1|^2+|F2|^2), whereas for dual model Fc=F1+F2 with phases included. Now, does this mean that I somehow have two types of twinning in this crystal - coherent (at 50%) and incoherent (at 10%)? Or is it that both description are correlated - in which case I don't understand why I get an additional drop when the two are combined. It may also be important that two-fold dimer axis are not exactly (but close) at the bisector - the polar angles reported by superpose are (87.91,-116.242,179.987). I'll appreciate any suggestions, Ed. -- 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 /
[ccp4bb] molecule on symmetry axis
Dear colleagues, I have a tartaric acid on a two fold axis with its two halves related by the two fold. How do I refine this in Phenix? Also I have a SO4 on a 3 fold with S and one O on tthe 3 fold. The other 3 oxygens are related by the 3-fold. How do I refine this in phenix? I can put S and one O occupancy 1, what occupancy do I put for the 3 oxygens that overlap their symmetry mates? And how do I maintain stereochemistry around the symmetry axis? These are not just one atom. For the tartaric acid the 2 fold goes through the middle of the bond. I could split it in two halves but I do not see how to keep stereochemistry. I would appreciate all suggestions. I apologize because the question should go to another newsgroup but I am still working with my subscription in phenixbb. Jackie Vitali
Re: [ccp4bb] molecule on symmetry axis
I try not to advertise SHELX too often on CCP4bb, but this is just the sort of disorder problem that small molecule crystallographers handle successfully and rather frequently with SHELX. The use of 'free variables' for tying occupancies together and restraining distances to be equal is something that it would be nice to have in phenix or refmac too. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 15 Oct 2010, Jacqueline Vitali wrote: Dear colleagues, I have a tartaric acid on a two fold axis with its two halves related by the two fold. How do I refine this in Phenix? Also I have a SO4 on a 3 fold with S and one O on tthe 3 fold. The other 3 oxygens are related by the 3-fold. How do I refine this in phenix? I can put S and one O occupancy 1, what occupancy do I put for the 3 oxygens that overlap their symmetry mates? And how do I maintain stereochemistry around the symmetry axis? These are not just one atom. For the tartaric acid the 2 fold goes through the middle of the bond. I could split it in two halves but I do not see how to keep stereochemistry. I would appreciate all suggestions. I apologize because the question should go to another newsgroup but I am still working with my subscription in phenixbb. Jackie Vitali
Re: [ccp4bb] vector and scalars
On Fri, Oct 15, 2010 at 8:11 PM, Douglas Theobald dtheob...@brandeis.edu wrote: Vectors are not only three-dimensional, nor only Euclidean -- vectors can be defined for any number of arbitrary dimensions. Your initial comment referred to complex numbers, for instance, which are 2D vectors (not 1-D). Obviously scalars are not 3-vectors, they are 1-vectors. And contrary to your earlier assertion, you can always represent complex numbers as vectors (in fortran, C, on paper, or whatever), and it is possible to define many different valid types of multiplication, exponentiation, logarithms, powers, etc. for vectors (and matrices as well). I didn't say that vectors are only 3D or only Euclidean (note my qualification 'Euclidean *or otherwise*'). I was stating that we're not talking here specifically about 1D (or 2D) vectors; my use of 3D is only an example, since my original example referred to structure factors which are usually defined in 3D reciprocal space. Quite obviously vectors can be generalised to any number of dimensions (as in the example below). Let's take a simple example of an operation that's trivial to express using complex numbers as scalars. Suppose we have 2 vectors of complex structure factors of equal dimension (n) and we want to form the (complex) scalar product. This kind of equation arises in, for example, the theory of direct methods. Let F = (F1, F2, F3, ... Fn) and G = (G1, G2, G3, ... Gn) Then the scalar product F.G = F1*G1 + F2*G2 + F3*G3 + ... Fn*Gn (or SUM [j=1 to n] Fj*Gj), where '+' and '*' here are the normal addition and multiplication operators on scalars (here complex of course). Note that the result of a scalar product of 2 vectors is by definition a scalar and here it's complex! Also note that the RHS can be programmed exactly as written, in fact something like: COMPLEX F, G, S S = 0 1READ (*,*,END=2) F, G S = S + F*G GOTO 1 2PRINT *,S END Now, how would you express the scalar product F.G in a way that could be programmed, using vector notation for all the complex numbers, and obviously you can only use operators that are defined for vectors, namely addition, subtraction, scalar multiplication, scalar and exterior product? Then when you've done that, how would you express a ratio of complex numbers (say F1/G1), again using only vector notation? -- Ian On Oct 15, 2010, at 12:40 PM, Ian Tickle wrote: Any vector, whether in the 'mathematical' or 'physical' sense as defined in Wikipedia, and which is defined on a 3D vector space (Euclidean or otherwise - which I hope is what were talking about), has by definition 3 elements (real or complex). This clearly excludes all scalars (real or complex) which have only 1 whatever the dimension of the space. Therefore it's plainly impossible for an entity in 3D space to be both a scalar and a vector at the same time. Your conclusion that scalars and complex numbers fulfil the axioms of a vector space is applicable only in the case of a 1D vector space, and therefore is not relevant. My original observation which started this thread was intended to be general one, not for a particular special case. -- Ian On Fri, Oct 15, 2010 at 5:17 PM, Douglas Theobald dtheob...@brandeis.edu wrote: On Oct 15, 2010, at 11:37 AM, Ganesh Natrajan wrote: Douglas, The elements of a 'vector space' are not 'vectors' in the physical sense. And there you make Ed's point -- some people are using the general vector definition, others are using the more restricted Euclidean definition. The elements of a general vector space certainly can be physical, by any normal sense of the term. And note that physical 3D space is not Euclidean, in any case. The correct Wikipedia page is this one http://en.wikipedia.org/wiki/Euclidean_vector Ganesh On Fri, 15 Oct 2010 11:20:04 -0400, Douglas Theobald dtheob...@brandeis.edu wrote: As usual, the Omniscient Wikipedia does a pretty good job of giving the standard mathematical definition of a vector: http://en.wikipedia.org/wiki/Vector_space#Definition If the thing fulfills the axioms, it's a vector. Complex numbers do, as well as scalars. On Oct 15, 2010, at 8:56 AM, David Schuller wrote: On 10/14/10 11:22, Ed Pozharski wrote: Again, definitions are a matter of choice There is no correct definition of anything. Definitions are a matter of community choice, not personal choice; i.e. a matter of convention. If you come across a short squat animal with split hooves rooting through the mud and choose to define it as a giraffe, you will find yourself ignored and cut off from the larger community which chooses to define it as a pig. -- === All Things Serve the Beam === David J. Schuller modern
Re: [ccp4bb] update REFMAC
Hi Ed, To upgrade the Refmac version that I am running from inside the CCP4i, I did the following mv $CCP4/bin/refmac5 $CCP4/bin/refmac5.5 cp refmacgfortran $CCP4/bin/refmac5.6 ln -s $CCP4/bin/refmac5.6 $CCP4/bin/refmac5 It seems to have worked fine. Is there more intelligent way of doing this? I asked the same question a few weeks and got a few helpful replies. Garib said you can replace $CBIN/refmac5 with refmac5.6, which is basically what you did. Or you can open ccp4i click System administration, select configure interface and jus below Give full path name for CCP4 programs to overcome name conflicts click Add a program There will appear two fields. On the right field type refmac5 and on the left field actual address of the program. Liz Potterton suggested that method as well. Sabine Schneider pointed out that the monomers dictionary lives at $CCP4/ccp4-6.1.3/lib/data/monomers/ and is set with the CLIBD_MON environment variable. Presumably you can just override the variable to point to a different directory and ccp4i will do the right thing. Boaz Shaanan suggested setting up your Refmac job using the current task interface, saving it as a .com file and then editing it by hand to add the additional parameters/flags available in Refmac 5.6. Finally Peter Cherepanov mentioned that you need the new fragment library and noted that version 5.6 uses LINK rather than LINKR. Note that I'm just a keyboard puncher, so your mileage may vary. Thanks to all for the suggestions. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] crystal growth
All the crystals I got for three different proteins in same condition looked similar. I think crystal morphology may vary with the crystallizing conditions.
